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PubMed1996

Mechanism of MAT alpha donor preference during mating-type switching of Saccharomyces cerevisiae.

During homothallic switching of the mating-type (MAT) gene in Saccharomyces cerevisiae, a- or alpha-specific sequences are replaced by opposite mating-type sequences copied from one of two silent donor loci, HML alpha or HMRa. The two donors lie at opposite ends of chromosome III, approximately 190 and 90 kb, respectively, from MAT. MAT alpha cells preferentially recombine with HMR, while MATa cells select HML. The mechanisms of donor selection are different for the two mating types. MATa cells, deleted for the preferred HML gene, efficiently use HMR as a donor. However, in MAT alpha cells, HML is not an efficient donor when HMR is deleted; consequently, approximately one-third of HO HML alpha MAT alpha hmr delta cells die because they fail to repair the HO endonuclease-induced double-strand break at MAT. MAT alpha donor preference depends not on the sequence differences between HML and HMR or their surrounding regions but on their chromosomal locations. Cloned HMR donors placed at three other locations to the left of MAT, on either side of the centromere, all fail to act as efficient donors. When the donor is placed 37 kb to the left of MAT, its proximity overcomes normal donor preference, but this position is again inefficiently used when additional DNA is inserted in between the donor and MAT to increase the distance to 62 kb. Donors placed to the right of MAT are efficiently recruited, and in fact a donor situated 16 kb proximal to HMR is used in preference to HMR. The cis-acting chromosomal determinants of MAT alpha preference are not influenced by the chromosomal orientation of MAT or by sequences as far as 6 kb from HMR. These data argue that there is an alpha-specific mechanism to inhibit the use of donors to the left of MAT alpha, causing the cell to recombine most often with donors to the right of MAT alpha.

Base Sequence↗

PubMed1991

Molecular characterization of eag: a gene affecting potassium channels in Drosophila melanogaster.

Genes encoding proteins involved in the function of the nervous system can be identified via mutations causing behavioral abnormalities. An example is ether à go-go (eag) in Drosophila melanogaster, which was identified originally as an X-linked mutation that displayed ether-induced leg-shaking behavior. Electrophysiological and genetic evidence suggests that the product of the eag locus is intimately involved in the normal functioning of one or more types of voltage-gated potassium channels. To initiate a molecular analysis of eag we first generated a collection of deletions to pinpoint its cytological location. On the basis of this location, we identified an existing inversion, In(1)sc29, with one breakpoint at the eag locus and the other in the scute (sc) complex. A genomic library was prepared from In(1)sc29 and screened with a genomic DNA fragment that spanned the sc breakpoint to isolate DNA from the eag region. Beginning from this starting point over 85 kb of DNA were isolated by chromosome walking. Three additional eag alleles, including two dysgenesis-induced insertion mutations and a gamma-ray-induced insertional translocation, were located on the molecular map of the eag locus by Southern blot analysis. The molecular defects associated with these alleles encompass a total of 27 kb within the chromosome walk. A 10-kb transcript derived from this region, which is expressed most abundantly in heads, was identified on Northern blots. Two different eag mutations separated by over 20 kb interrupt the same transcript identifying it as the likely eag message. cDNAs representing a portion of this transcript have been isolated.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗

PubMed2002

Structures of neat and hydrated 1-octanol from computer simulations.

Molecular dynamics computer simulations of 1-octanol and its mixtures with water have been performed. The liquid is composed of regions enriched in either hydrocarbons or hydroxyl groups. In neat octanol, the hydroxyl groups form clusters of long, thin chains. Upon the addition of water, the clusters become longer and more spherical, forming a structure that can be described as consisting of "overlapping elongated inverse micelles". The structures of the mixtures obtained at different hydration levels are consistent with those of experimental diffraction studies of water/octanol mixtures and previous computer simulations of neat and water-saturated octanol. The saturation point of the model has been calculated using the cavity-bias particle insertion method. The solubility of water in octanol is slightly too low compared to experimental results, and suggestions for possible improvements to the force field are made.

1-Octanol↗

PubMed2003

Intronic L1 insertion and F268S, novel mutations in RPS6KA3 (RSK2) causing Coffin-Lowry syndrome.

Two novel mutations of the ribosomal S6 kinase 2 gene (also known as RSK2) have been identified in two unrelated patients with Coffin-Lowry syndrome. The first mutation consists of a de novo insertion of a 5'-truncated LINE-1 element at position -8 of intron 3, which leads to a skipping of exon 4, leading to a shift of the reading frame and a premature stop codon. The L1 fragment (2800 bp) showed a rearrangement with a small deletion, a partial inversion of the ORF 2, flanked by short direct repeats which duplicate the acceptor splice site. However, cDNA analysis of the patient shows that both sites are apparently not functional. The second family showed the nucleotide change 803T>C in exon 10, resulting in the F268S mutation. This mutation was detected in two monozygotic twin patients and in their mother, who was mildly affected. The patients fulfill the clinical criteria of the syndrome, and therefore the mutation provides further support for the importance of phenylalanine at position 268, which is highly conserved in the protein kinase domain of many serine-threonine protein kinases.

Adult↗

PubMed1984

Rearranged sequences of a human Kpn I element.

The complete nucleotide sequence of a human Kpn I element inserted into alpha-satellite DNA is presented. This sequence reveals several features of interest. First, a large block of DNA normally associated with Kpn I elements has been deleted. Second, the order of the remaining sequences is permuted in a manner that cannot be accounted for by simple inversion. Third, a significant open reading frame of 675 bases is detected.

Base Composition↗

PubMed2006

Female hemophilia A heterozygous for a de novo frameshift and a novel missense mutation of factor VIII.

BACKGROUND: Hemophilia A (HA) is an X-chromosome-linked recessive disorder. AIM: We report the case of a female HA patient with a moderate decrease of factor (F) VIII activity and antigen (FVIII:C 3.4%, FVIII:Ag 4.2%) and severe bleeding symptoms. METHODS: The patient's father had mild FVIII deficiency (FVIII:C 6.9%, FVIII:Ag 7.4%), and her mother had normal FVIII activity. The von Willebrand disease antigen and von Willebrand factor ristocetin cofactor activity were normal in all family members. The genomic DNA was extracted from the peripheral blood lymphocytes of the patient and her family members. Long-distance polymerase chain reaction (PCR) was employed to screen for the intron 22 inversion of the FVIII coding gene (F8). The F8 coding sequence was amplified with PCR and sequenced with an automatic sequencer. RESULTS: Two heterozygous mutations were identified in the patient: one a substitution of nucleotide 5981T by C that leads to a missense mutation Leu1975Pro, and the other an insertion of an 'A' between nucleotides 3,637 and 3,638 (3637_3638insA) that shifts the reading frame and predicts a premature stop codon downward. The mutation Leu1975Pro was identified in the father's F8; however, 3637_3638insA was a de novo mutation that occurred in the patient's maternal-derived F8. Real-time PCR was applied to analyze the level of ectopically F8 gene transcripts in the peripheral lymphocytes of family members. The ectopic transcripts of F8 of the patient were less abundant than the normal control (patient:normal control ratio 0.67), whereas her parents showed no significant difference from the normal control. CONCLUSION: The FVIII deficiency of the HA patient resulted from a de novo occurrence of a frameshift 3637_3638insA in her maternal-derived F8 and a novel missense mutation Leu1975Pro inherited from her father.

Child↗

PubMed1984

Location and analysis of nucleotide sequences at one end of a putative lac transposon in the Escherichia coli chromosome.

A segment of Escherichia coli DNA that contained a discontinuity of homology with Salmonella typhimurium DNA was isolated. The segment, 1,430 base pairs long, was derived from one end of the lac "loop," a region of about 12 kilobase pairs of E. coli DNA, including the lac operon which has no detectable homology with S. typhimurium DNA (K. Lampel and M. Riley, Mol. Gen. Genet. 186:82-86, 1982). The nucleotide sequence of the 1,430-base-pair segment of DNA was determined. The location of the junction of discontinuity of homology within the segment was established by hybridization experiments. Nucleotide sequences at or near the junction were determined to be similar to sequences that are involved in site-specific inversion in S. typhimurium, E. coli, phage P1, and phage Mu. Similar sequences are also present within the terminal inverted repeat sequences of transposon Tn5 and at the V-D-J joining sequences of eucaryotic immunoglobulin genes. Therefore, the lac operon, together with flanking DNA, may have been inserted into the E. coli chromosome at one time via a site-specific recombination event. Rearrangement events of this kind undoubtedly have played a significant role in the evolutionary divergence of chromosomal DNAs.

Base Composition↗

PubMed1989

Nucleotide sequences required for Tn3 transposition immunity.

The Tn3 transposon inserts at a reduced frequency into a plasmid already containing a copy of Tn3, a phenomenon known as transposition immunity. The cis-acting site on Tn3 responsible for immunity was mapped by deletions from each side to be within the terminal 38-base-pair sequence that is inversely repeated at the ends of Tn3. Two palindromic sequences are present in the essential part of this region. Some deletions conferred only partial immunity, and others conferred negative immunity. Multiple copies of partially immune ends conferred additional immunity. No other part of Tn3 was necessary for immunity.

Base Sequence↗

PubMed2004

Transposition of reversed Ac element ends generates chromosome rearrangements in maize.

In classical "cut-and-paste" transposition, transposons are excised from donor sites and inserted at new locations. We have identified an alternative pathway in which transposition involves the 5' end of an intact Ac element and the 3' end of a nearby terminally deleted fAc (fractured Ac). The Ac and fAc elements are inserted at the maize p1 locus on chromosome 1s in the same orientation; the adjacent ends of the separate elements are thus in reversed orientation with respect to each other and are separated by a distance of approximately 13 kb. Transposition involving the two ends in reversed orientation generates inversions, deletions, and a novel type of local rearrangement. The rearrangement breakpoints are bounded by the characteristic footprint or target site duplications typical of Ac transposition reactions. These results demonstrate a new intramolecular transposition mechanism by which transposons can greatly impact genome evolution.

Base Sequence↗

PubMed2005

Targeting of c-Met and urokinase expressing human glioma cell lines by retrovirus vector displaying single-chain variable fragment antibody.

Amphotropic retroviruses with modified envelope displaying single-chain antibody fragment (scFv) directed against the c-Met receptor were recently generated and found to efficiently and selectively deliver genes into hepatocarcinoma cells. A large proportion of human gliomas also frequently overexpresses c-Met. We therefore explored the possibility of infecting glioma cells using such retroviruses bearing an scFv directed against c-Met. In one construct, a urokinase (uPA) cleavage site was inserted between the scFv and the envelope. We assessed the transduction by these chimeric viruses of a panel of seven human glioma cell lines that we characterized for their c-Met and uPA levels. We found that abundance of the c-Met receptor and viral infection were inversely correlated if we used the retrovirus displaying scFv directed against c-Met, suggesting that the chimeric virus binds preferentially to the c-Met receptor, resulting in virus sequestration. Addition of the uPA site between the scFv moiety and the envelope restored the infectivity of the virus, consistent with a "two-step" infection process: (1) virus binding to the c-Met receptor, (2) cleavage of the scFv moiety by uPA, enabling the virus to dissociate from c-Met and entry into the cells via the Pit-2 receptor. Our study has significant implications for the design of targeting strategies for gliomas expressing high levels of c-Met.

Antibodies↗

PubMed1991

The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding.

The 98-amino acid Fis protein from Escherichia coli functions in a variety of reactions, including promotion of Hin-mediated site-specific DNA inversion when bound to an enhancer sequence. It is unique among site-specific DNA-binding proteins in that it binds to a large number of different DNA sequences, for which a consensus sequence is difficult to establish. X-ray crystal structure analyses have been carried out at 2.3 A resolution for wild-type Fis and for an Arg-89----Cys mutant that does not stimulate DNA inversion. Each monomer of the Fis dimer has four alpha-helices, A-D; the first 19 residues are disordered in the crystal. The end of each C helix is hydrogen bonded to the beginning of helix B' from the opposite subunit in what effectively is one long continuous, although bent, helix. The four helices, C, B', C', and B, together define a platform through the center of the Fis molecule: helices A and A' are believed to be involved with Hin recombinase on one side, and helices D and D' interact with DNA lying on the other side of the platform. Helices C and D of each subunit comprise a helix-turn-helix (HTH) DNA-binding element. The spacing of these two HTH elements in the dimer, 25 A, is too short to allow insertion into adjacent major grooves of a straight B-DNA helix. However, bending the DNA at discrete points, to an overall radius of curvature of 62 A, allows efficient docking of a B-DNA helix with the Fis molecule. The proposed complex explains the experimentally observed patterns of methylation protection and DNase I cleavage hypersensitivity. The x-ray structure accounts for the effects of mutations in the Fis sequence. Those that affect DNA inversion but not DNA binding are located within the N-terminal disordered region and helix A. This inversion activation domain is physically separated in the Fis molecule from the HTH elements and may specify a region of contact with the Hin recombinase. In contrast, mutations that affect HTH helices C and D, or interactions of these with helix B, have the additional effect of decreasing or eliminating binding to DNA.

Amino Acid Sequence↗

PubMed2004

Concerning the mechanism of the ring opening of propylene oxide in the copolymerization of propylene oxide and carbon dioxide to give poly(propylene carbonate).

The reactions between (TPP)AlX, where TPP = tetraphenylporphyrin and X = Cl, O(CH(2))(9)CH(3), and O(2)C(CH(2))(6)CH(3), and propylene oxide, PO, have been studied in CDCl(3) and have been shown to give (TPP)AlOCHMeCH(2)X and (TPP)AlOCH(2)CHMeX compounds. The relative rates of ring opening of PO follow the order Cl > OR > O(2)CR, but in the presence of added 4-(dimethylamino)pyridine, DMAP (1 equiv), the order is changed to O(2)CR > OR. From studies of kinetics, the ring opening of PO is shown to be first order in [Al]. Carbon dioxide inserts reversibly into the Al-OR bond to give the compound (TPP)AlO(2)COR, and this reaction is promoted by the addition of DMAP. The coordination of DMAP to (TPP)AlX is favored in the order O(2)C(CH(2))(6)CH(3) > O(2)CO(CH(2))(9)CH(3) >> O(CH(2))(9)CH(3). The microstructure of the poly(propylene carbonate), PPC, formed in the reactions between (TPP)AlCl/DMAP and (R,R-salen)CrCl and rac-PO/S-PO/R-PO and CO(2), has been investigated by (13)C [(1)H] NMR spectroscopy. The ring opening of PO is shown to proceed via competitive attack on the methine and methylene carbon atoms, and furthermore attack at the methine carbon occurs with both retention and inversion of stereochemistry. On the basis of these results, the reaction pathway leading to ring opening of PO can be traced to an interchange associative mechanism, wherein coordination of PO to the electrophilic aluminum atom occurs within the vicinity of the Al-X bond (X = Cl, OR, O(2)CR, or O(2)COR). The role of DMAP is two-fold: (i) to labilize the trans Al-X bond toward heterolytic behavior, and (ii) to promote the insertion of CO(2) into the Al-OR bond.

Journal Article↗

PubMed1972

Structure of inserted bacteriophage Mu-1 DNA and physical mapping of bacterial genes by Mu-1 DNA insertion.

It is shown, by electron microscope observation of the structures of heteroduplexes, that Mu-1 DNA inserted into the bacterial episomes Flac and F(8)[1] is collinear with, rather than a circulation permutation of, the DNA of the mature Mu-1 bacteriophage. Observation of the position of the inserted Mu defines a point within the gene that has been inactivated (the lacI gene for Flac and a transfer gene in F(8)[1] in these particular instances). These examples illustrate a new, general method for physical gene mapping. The episome with Mu DNA inserted into F(8)[1] [i.e., F(8)[1](Mu)], although derived from a single colony, is heterogeneous in that a self-renatured sample shows a nonhomology loop of length 3.0 kb. This nonhomology loop, which has previously been observed in mature Mu-1 DNA, is due to an inversion.

Chromosome Mapping↗

PubMed1990

A direct surgical approach to correct the inverted nipple.

Inverted nipples are cosmetically unpleasing to the patient and can become inflamed due to mechanical difficulty with cleaning the nipple-areola complex. A surgical technique for the permanent repair of inverted nipples is described. The rationale for the surgical approach is that the major pathophysiologic basis for nipple inversion is shortened lactiferous ducts. Briefly outlined, under local anesthesia, the nipple is everted with a skin hook and held in gentle traction while a small incision is made on each side at the nipple-areola junction. Breast ducts are then divided by sharp dissection, and a drain is inserted through the tunnel under the nipple. The drain is removed in 7 to 10 days. The patient must be informed before the procedure that breast-feeding will not be possible afterward because breast ducts will be permanently divided. Advantages to the procedure are (1) no scars on the areola, (2) no stricture from sutures, (3) adequate blood and nerve supply to the nipple, and (4) decreased risk of hematoma.

Adult↗

PubMed2000

Comparison of contractile properties of single motor units in human intrinsic and extrinsic finger muscles.

1. The purpose of the present study was to compare the contractile properties of single motor units in the intrinsic (short) and extrinsic (long) finger muscles in awake human subjects using intraneural motor axon stimulation. 2. Twitch properties were measured for 17 intrinsic and 11 extrinsic motor units by selective stimulation of a single motor axon in the ulnar or the median nerve. Force was measured from the appropriate digit, just distal to the muscle's point of insertion and single unit EMG was recorded with surface electrodes. Force-frequency relationships (2-100 Hz) were established for 16 of these units (7 intrinsic, 9 extrinsic). Across the 16 motor units for which force-frequency data were obtained, twitch contraction time (63.7 +/- 6.0 ms, mean +/- s.e.m.) was inversely correlated with the frequency required to generate half-maximum tetanic force (12.0 +/- 1.1 Hz). 3. We found no systematic differences between the contractile properties of intrinsic and extrinsic motor units. There was no evidence of a bimodal distribution into large/small or fast/slow units based on maximum force or contraction times, although both fast and slow motor units were encountered. 4. The peak slope of the sigmoidal force-frequency relationship for intrinsic motor units (9.1 and 4.4-12.9 mN Hz-1, median and interquartile range) was significantly higher than that for extrinsic motor units (2.9 and 2.3-3.1 mN Hz-1; P = 0.028), i.e. greater force steps were produced by the intrinsic motor units for a given change in stimulation frequency. This difference suggests that motor units in the intrinsic muscles of the hand are more sensitive to modulating force output by changes in motoneurone firing rates than are those in the extrinsic muscles. This reflects the important role of the intrinsic hand muscles in the fine manipulation of objects.

Adolescent↗

PubMed1998

Influence of different trocar tips on abdominal wall penetration during laparoscopy.

Most trocars currently used to place a cannula through the abdominal wall have a conical or pyramidal tip. Because the risk of inadvertent injury along with removal of the cannula is probably related to (a) the force needed to traverse the abdominal wall, (b) the force needed to remove the trocar, and (c) the defect in the abdominal wall, the optimum configuration of the penetrating tip should be determined. The entry force needed to perforate the abdominal wall, the removal force necessary to remove the trocar, and the defect in the abdominal wall were measured in a porcine model under standardized conditions (general anesthesia, 12 mmHg pneumoperitoneum). Nineteen trocars (six disposable, seven reusable, six custom-made) have been tested. They were divided into six groups according to the shape of the tip (conical, pyramidal, or a combination). The entry force (F = 25.6, p < 0.0001) and the removal force (F = 5.1, p < 0.01) were related to the shape of the tip. Conical tips needed a higher force than purely pyramidal tips. The abdominal defect was also different between groups (F = 6.5, p < 0. 001). The trocar with a pyramidal shape caused a greater defect than conical tips. The defect in the abdominal wall was inversely related to the entry force (r = -0.55, p < 0.001) and to the removal force (r = -0.57, p < 0.001). There is not an optimum configuration of a simple push-through trocar with a low entry force and a high removal force. Some kind of a conical tip is recommended for insertion of trocars under direct view.

Abdominal Muscles↗

PubMed2004

Crystal structure of bet3 reveals a novel mechanism for Golgi localization of tethering factor TRAPP.

Transport protein particle (TRAPP) is a large multiprotein complex involved in endoplasmic reticulum-to-Golgi and intra-Golgi traffic. TRAPP specifically and persistently resides on Golgi membranes. Neither the mechanism of the subcellular localization nor the function of any of the individual TRAPP components is known. Here, the crystal structure of mouse Bet3p (bet3), a conserved TRAPP component, reveals a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Charge-inversion mutations on the flat surface of the highly conserved yeast Bet3p led to conditional lethality, incorrect localization and membrane trafficking defects. A channel-blocking mutation led to similar defects. These data delineate a molecular mechanism of Golgi-specific targeting and anchoring of Bet3p involving the charged surface and insertion of a Golgi-specific hydrophobic moiety into the channels. This essential subunit could then direct other TRAPP components to the Golgi.

Acylation↗

PubMed2006

Renner-Teller quantum dynamics of the N(2D) + H2-->NH + H reaction.

We present the Born-Oppenheimer (BO) and Renner-Teller (RT) quantum dynamics of the reaction (14)N((2)D)+(1)H(2)(X (1)Sigma(g) (+))-->NH(X (3)Sigma(-))+H((2)S), considering the NH(2) electronic states X (2)B(1) and A (2)A(1). These states correlate to the same (2)Pi(u) linear species, are coupled by RT nonadiabatic effects, and give NH(X (3)Sigma(-))+H and NH(a (1)Delta)+H, respectively. We develop the Hamiltonian matrix elements in the R embedding of the Jacobi coordinates and in the adiabatic electronic representation, using the permutation-inversion symmetry, and taking into account the nuclear-spin statistics. Collision observables are calculated via the real wave-packet (WP) and flux methods, using the potential-energy surfaces of Santoro et al. [J. Phys. Chem. A 106, 8276 (2002)]. WP snapshots show that the reaction proceeds via an insertion mechanism, and that the RT-WP avoids the A (2)A(1) potential barrier, jumping from the excited to the ground surface and giving mainly the NH(X (3)Sigma(-)) products. X (2)B(1) BO probabilities and cross sections show large tunnel effects and are approximately four to ten times larger than the A (2)A(1) ones. This implies a BO rate-constant ratio k(X (2)B(1))k(A (2)A(1)) approximately 10(5) at 300 K, i.e., a negligible BO formation of NH(a (1)Delta). When H(2) is rotationally excited, RT couplings reduce slightly the X (2)B(1) reaction observables, but enhance strongly the A (2)A(1) reactivity. These couplings are important at all collision energies, reduce the collision threshold, and increase remarkably reaction probabilities and cross sections. The RT k(A (2)A(1)) is thus approximately 3.3 order of magnitude larger than the BO value, and degeneracy-averaged, initial-state-resolved rate constants increase by approximately 13% and by approximately 47% at 300 and 500 K, respectively. Owing to an overestimation of the X (2)B(1) potential barrier, the calculated thermal rate is too low with respect to that observed, but we obtain a good agreement by shifting down the calculated cross section.

Journal Article↗