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PubMed1990

Identification, cloning, and sequencing of piv, a new gene involved in inverting the pilin genes of Moraxella lacunata.

Moraxella lacunata is a bacterium that is a causative agent of human conjunctivitis and keratitis. We have previously cloned the Q and I pilin (formerly called beta and alpha pilin) genes of Moraxella bovis and determined that an inversion of 2 kilobases (kb) of DNA determines which pilin gene is expressed. Using an M. bovis pilin gene as a hybridization probe to screen a lambda ZAP library of M. lacunata DNA, we have isolated a clone that not only contains the entire type 4 pilin gene inversion region of M. lacunata but inverts the 2-kb region on a plasmid subclone (pMxL1) in Escherichia coli. Deletion derivatives of pMxL1 yielded some plasmids that still had the entire inversion region but were phase locked into one or the other of the two potential orientations. Similarly, insertions of a 2-kb streptomycin-resistant element (omega) within some regions outside of the inversion also resulted in phase-locked plasmids. These deletions and insertions thus localize a probable invertase necessary for the inversion event. The region was sequenced, and an open reading frame with over 98% DNA sequence homology to an open reading frame that we previously found in M. bovis and called ORF2 appeared to be a strong candidate for the invertase. This conclusion was confirmed when a plasmid containing the M. bovis ORF2 supplied, in trans, the inversion function missing from one of the M. lacunata phase-locked inversion mutants. We have named these putative invertase genes piv(ml) (pilin inversion of M. lacunata) and piv(mb) (pilin inversion of M. bovis). Despite previously noted sequence similarities between the M. bovis sites of inversion and those of the Hin family of invertible segments and a 60-base-pair region within the inversion with 50% sequence similarity to the cin recombinational enhancer, there is no significant sequence similarity of the Piv invertases to the Hin family of invertases.

Amino Acid Sequence↗
PubMed1990

Synapsis in single and double heterozygotes for partially overlapping inversions in chromosome 1 of the house mouse.

Electron microscopic (EM) analysis of synaptonemal complexes (SC) in single and double heterozygotes for the partially overlapping inversions In(1)1Icg, In(1)1Rk and In(1)12Rk in chromosome 1 of the house mouse reveals that synapsis and synaptic adjustment are dependent on the size and location of the inversions and interaction between the latter. Is(1)1Icg contains insertions of the inverted repeats Is(HSR;1C5)1Icg and Is(HSR;1D)2Icg and an inverted euchromatic region. Synaptic adjustment of the D-loops by shortening of the asynapsed segments of the lateral elements belonging to the insertions occurs at the late zytogene to early pachytene stage. Synaptic adjustment of the inversion loops takes place at early to late pachytene. A delay in adjustment was found in the double heterozygotes In(1)1Icg/In(1)1Rk and In(1)1Icg/In(1)12Rk. A correspondence between the lifespan of asynapsis in inverted regions and the probability of association of XY and heteromorphic bivalents was revealed.

Animals↗
PubMed1981

Techniques for manipulating chromosomal rearrangements and their application to Drosophila melanogaster. I. Pericentric inversions.

Techniques have been developed for manipulating pericentric inversions in Drosophila that are based on the lethality of grossly aneuploid zygotes and the existence of recombinationally interconvertible genotypes for any heterozygous inversion complex: males of some of these genotypes will produce only aneuploid sperm, which can be used to rescue complementary aneuploid ova and selectively recover recombinational derivatives of inversions. Markers can be recombined into inversions through a sequence of selected single exchanges, and a novel type of duplication can be synthesized from overlapping inversions that has the characteristics of both insertional and tandem duplications; there are also applications to half-tetrad analyses.--Two cytogenetic screens are developed: (1) the dominant lethality of a large insertional-tandem duplication can be reverted by deletional events that give rise to net deficiencies or duplications, and (2) deficiencies and tandem duplications in proximal regions can be selectively recovered as the results of unequal exchanges within an inversion loop. Recombinants have been recovered between breakpoints separated by distances of as little as fifty bands, arguing against the existence of some small number of sites necessary for the initiation of recombinational pairing. In several instances, hyperploids for four to six numbered divisions were observed to be fertile in both sexes.

Aneuploidy↗
PubMedDate not supplied

Middle-vault narrowing in the wide nasal dorsum: the "Reverse Spreader" technique.

The middle vault is a transition zone between the nasal tip and nasal bones and plays an important role in profile, tip projection, tip rotation, and tip support. This report presents an alternative to conventional techniques specific to the middle nasal vault for a patient population with particular nasal features. A narrow middle vault with internal nasal valve collapse is functionally and aesthetically addressed by the insertion of spreader grafts. However, the inverse of this situation is sometimes encountered. A patient with a broad middle vault and without internal nasal valve collapse will benefit from reduction of the horizontal width of the cartilaginous dorsum, which is in effect the reverse of spreader grafts. This effect is achieved by excising a vertical wedge-shaped strip of cartilage that follows the length of the upper lateral cartilage at the junction of the upper lateral cartilage and the dorsal nasal septum.

Cartilage↗
PubMed1987

Effect of the direction of DNA replication on mutagenesis by N-methyl-N'-nitro-N-nitrosoguanidine in adapted cells of Escherichia coli.

The methylating agent N-methyl-N'-nitro-N-nitrosoguanidine preferentially induces G:C to A:T transitions at DNA base pairs with the G in one particular strand of the cI gene in a lambda prophage, in this case the nontranscribed strand, in Escherichia coli cells in which the adaptive response is induced. The same preference is found for the cI gene inserted in the genome in the inverse orientation, so the differential effect is not caused by the direction of motion of the DNA replicating fork.

Base Composition↗
PubMed1992

G-banding analysis of radiation-induced chromosome damage in lymphocytes of Hiroshima A-bomb survivors.

The present report describes the G-band analysis of somatic chromosomes in lymphocytes from 63 A-bomb survivors in Hiroshima to determine the type and frequency of radiation-induced chromosome aberrations. (1) The cells with stable-type chromosome aberrations (Cs cells) predominated among the aberrant cells, and showed a dose-dependent increase. All stable chromosome aberrations were classified into nine categories: reciprocal translocations, translocations of complex type, insertions, complex exchanges, peri- and paracentric inversions, terminal and interstitial deletions, and unidentified rearrangements. The frequencies of aberrations were found to increase with increasing dose for all aberration categories. Reciprocal translocations predominate in all dose ranges and among the chromosome aberrations classified. (2) The linear model was fitted to test the dose-response relationship for Cs cell frequencies. Employing a constant neutron RBEs of 10, an estimated linear slope of 15.2%/Sv was obtained for DS86 bone marrow dose with an intercept of 2.9% at dose 0. (3) Statistical analysis of data on 3,370 break sites showed good correlations between relative DNA content and the distribution of chromosome breaks involved in translocations, although the involvement of chromosome 1 is significantly higher.

Bone Marrow↗
PubMed1985

Nonreciprocal exchange between alleles of the yeast mitochondrial 21S rRNA gene: kinetics and the involvement of a double-strand break.

A 1.1 kb intron containing an open reading frame (ORF) in one allele (omega+) of the yeast mitochondrial 21S rRNA gene is nearly quantitatively inserted in crosses into a 21S rRNA allele lacking that intron (omega-). We have determined that this nonreciprocal exchange initiates soon after cells fuse to form zygotes and is complete by 10-16 hr after mating. We have discovered a unique in vivo double-strand cut in omega- mitochondrial DNA (mtDNA) at or near the site of intron insertion that is implicated in the process. Markers flanking the intron insertion site are coconverted with frequencies inversely proportional to their distance from that site. There is no net conversion of omega- to omega+ in crosses between petites retaining these alleles, nor do we observe the unique double-strand cut in the mtDNA from zygotes of such crosses. The data suggest that a translation product of the intron ORF is required for the double-strand cut and nonreciprocal recombination at omega.

Alleles↗
PubMed1989

Identification of a 220-kb insertion into the Duchenne gene in a family with an atypical course of muscular dystrophy.

Most known mutations in the gene region responsible for Duchenne or Becker muscular dystrophy are deletions of varying extent. Here we describe a 220-kb insertion within the DMD/BMD gene that cosegregates with a somewhat atypical course of muscular dystrophy in a pedigree. The insertion is demonstrated by field-inversion gel electrophoresis as an enlarged SfiI fragment hybridizing to probe J-Bir, while neighboring SfiI fragments (detected by probes PERT 87 and J-66) are unchanged. Hybridization with DMD c-DNA probes did not reveal alterations in coding sequences. In this pedigree, the altered SfiI fragments provide convenient markers for carrier identification.

Blotting, Southern↗
PubMed2004

Impact on active scope deflection and irrigation flow of all endoscopic working tools during flexible ureteroscopy.

OBJECTIVE: Flexible ureteroscopy is nowadays an alternative effective option for treatment of upper urinary tract stones, especially in the lower renal pole. Access in this case is often limited by active deflection capabilities of the instrument which is always deteriorated by the passage of different tools through the working channel. Insertion of them limits also the irrigation flow and so that the visibility. These deteriorations vary largely following the tool inserted. We performed an in vitro evaluation of deterioration of active deflection, possibility of tool insertion in maximal active deflection and irrigation flow in 6 different flexible ureteroscopes with almost all of tools available. METHODS: A total of 546 measures of maximal deflection, test of passage of tools in maximal deflection and measures of irrigation flow passage through the working channel were made on 6 different ureteroscopes, the ACMI DUR-8, the ACMI DUR-8 "Elite", the Karl Storz 11274 AA, the Karl Storz 11278 AU1 "Flex-X", the Wolf 7325.172 and the Olympus URF/P-3 without any tool inserted and with 22 different tools (14 extraction devices and 8 lithotripsy probes). RESULTS: Larger caliber tools resulted in more deflection degradation than smaller ones but it is more evident in case of use of non-nitinol tools instead of the nitinol ones. Generally lithotripsy probes affected active deflection more than nitinol extractions tools but different brand laser fibres present different results. Usually 1.6 and 1.9F electro hydraulic probes offer a slightly better deflection than does the 200micro laser fibre. Ballistic shock probes are so stiff that can not be used for treating lower renal pole stones. CONCLUSIONS: An array of different instruments are nowadays available for upper renal endoscopic treatment but they differ largely on stiffness and on obstruction to irrigation flow. Laser probes are very problematic to insert in the already deflected instruments, something that is less evident with the EHL probes and the smaller nitinol extraction tools. Irrigation flow is inversely proportional to the diameter of the tool inserted. Tools with a diameter of 3 French or more block totally the flow.

Equipment Design↗
PubMed2004

Overly wide cartilaginous middle vault.

Any maneuver in rhinoplasty that alters the ULCs should be based on a preoperative analysis of the patient's functional complaints and aesthetic characteristics. All techniques should be harmonious with the desired postsurgical result. The majority of established procedures to alter the middle vault focus on dorsal hump reduction, correction of internal nasal valve collapse, or correction of a twisted nose with the use of spreader grafts [9 12]. Although the latter two techniques achieve satisfying functional results, they can have the effect of broadening the middle third of the nose. Reduction of the dorsal height of the middlenasal vault by way of horizontal shaving of the ULC scan sometimes result in functional compromise by narrowing the nasal valve [13]. Each technique has advantages when performed with appropriate indications. For example, a narrow middle vault with internal nasal valve collapse is functionally and aesthetically addressed by the insertion of spreader grafts; however, the inverse of this situation is sometimes encountered. A patient who has a broad middle vault without internal nasal valve collapse will benefit from reduction of the horizontal width of the cartilaginous dorsum, which is, in effect,the reverse of spreader grafts [2]. A select patient population requires aesthetic refinement of the middle vault in a way that avoids functional compromise. This reverse spreader technique has probably been applied clinically by others, but it is has not been reflected in the literature before this year [2]. Johnson and Toriumi have described a similar maneuver in addressing a wide bony dorsum, encouraging the surgeon to "think vertically" [8]. Likewise, Toriumiand Ries have described a selective tangential shaving of the convex side dorsal septum to assist in correction of the C-shaped deformity [11]. In the setting of a wide middle vault, the reverse spreader technique is a useful alternative to dorsal augmentation, which creates the illusion of a narrower dorsum [ 14]; however, it should be noted that patients who have a wide, low dorsum might benefit more from dorsal augmentation than from this technique. Caution should be employed in individuals who have internal nasal valve compromise, which can be exacerbated by this maneuver.

Esthetics↗
PubMed2007

Bilayer mechanical properties regulate the transmembrane helix mobility and enzymatic state of CD39.

CD39 can exist in at least two distinct functional states depending on the presence and intact membrane integration of its two transmembrane helices. In native membranes, the transmembrane helices undergo dynamic rotational motions that are required for enzymatic activity and are regulated by substrate binding. In this study, we show that bilayer mechanical properties regulate conversion between the two enzymatic functional states by modulating transmembrane helix dynamics. Alteration of membrane properties by insertion of cone-shaped or inverse cone-shaped amphiphiles or by cholesterol removal switches CD39 to the same enzymatic state that removal or solubilization of the transmembrane domains does. The same membrane alterations increase the propensity of both transmembrane helices to rotate within the packed structure, resulting in a structure with greater mobility but not an altered primary conformation. Membrane alteration also abolishes the ability of the substrate to stabilize the helices in their primary conformation, indicating a loss of coupling between substrate binding and transmembrane helix dynamics. Removal of either transmembrane helix mimics the effect of membrane alteration on the mobility and substrate sensitivity of the remaining helix, suggesting that the ends of the extracellular domain have intrinsic flexibility. We suggest that a mechanical bilayer property, potentially elasticity, regulates CD39 by altering the balance between the stability and flexibility of its transmembrane helices and, in turn, of its active site.

Antigens, CD↗
PubMed2006

Photochemical electron transfer through [corrected] the interface of hybrid films of titania nano-sheets and mono-dispersed spherical mesoporous silica particles.

Photochemical Electron Transfer (ET) between an organic dye, the porphyrin derivative TMPyP, and an electron acceptor, methyl viologen MV2+, have been investigated at the interface of two different inorganic films, i.e., layered titania nano-sheets (TNS) and a monolayer film of spherical and mono-dispersed mesoporous silica (sMPS) particles (ca. 0.5 microm). TMPyP ions were intercalated within the sMPS nano-cavities to form (TMPyP-sMPS) while MV2+ ions were intercalated into the TNS interlayers to form (MV2+-TNS). The (TMPyP-sMPS) and (MV2+-TNS) films were then stacked on a silica substrate in this order to form a (MV2+-TNS)/(TMPyP-sMPS) film and, upon UV light irradiation, ET could be induced. However, when this film was stacked inversely, i.e., for the (TMPyP-sMPS)/(MV2+-TNS) films on a silica substrate, no photoinduced ET were observed. Interestingly, however, even for this photo-inactive inversely stacked film, ET could be generated by inserting a gold vapor-deposited layer between the (MV2+-TNS) and (TMPyP-sMPS) films. The conjugation conditions at the interface of the inversely stacked (TMPyP-sMPS)/(MV2+-TNS) hybrid film were, thus, confirmed to strongly affect the photoinduced electron transfers and their efficiencies.

Biocompatible Materials↗
PubMed2026

SynFlow: an interactive online genome structural variant viewer.

MOTIVATION: Structural variations (SVs), including inversions, translocations (TRAs), duplications, and large insertions or deletions, are key drivers of genome evolution and phenotypic diversity. With the increasing number of high-quality, chromosome-scale genome assemblies, the ability to detect and interpret SVs has become a crucial aspect of modern genomics. While SV detection has advanced, most visualization methods produce static plots that fall short when researchers, particularly in comparative genomics, need to interactively explore large datasets, zoom into specific genomic regions, or dynamically filter structural events in real time. RESULTS: To address this gap, we introduce SynFlow, a lightweight, web-based interactive application specifically designed for exploring and visualizing SVs identified by SyRI. We demonstrate that SynFlow can reproduce complex static synteny plots published in literature, but transforms them into dynamic, shareable visualizations that support real-time filtering, reordering, and deep exploration of specific SVs, including TRAs. SynFlow is available as a web server and offers multiple entry points: browsing precomputed datasets (e.g. banana and grapevine genomes), uploading user-provided SyRI outputs, or running an integrated workflow to produce and visualize SVs on the fly. AVAILABILITY AND IMPLEMENTATION: https://synflow.southgreen.fr; source code https://github.com/SouthGreenPlatform/synflow; preprocessing Snakemake workflow https://gitlab.cirad.fr/agap/cluster/snakemake/synflow.

Software↗
PubMed1999

Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids.

Corn and rice genetic linkage map alignments were extended and refined by the addition of 262 new, reciprocally mapped maize cDNA loci. Twenty chromosomal rearrangements were identified in maize relative to rice and these included telomeric fusions between rice linkage groups, nested insertion of rice linkage groups, intrachromosomal inversions, and a nonreciprocal translocation. Maize genome evolution was inferred relative to other species within the Panicoideae and a progenitor maize genome with eight linkage groups was proposed. Conservation of composite linkage groups indicates that the tetrasomic state arose during maize evolution either from duplication of one progenitor corn genome (autoploidy) or from a cross between species that shared the composite linkages observed in modern maize (alloploidy). New evidence of a quadruplicated homeologous segment on maize chromosomes 2 and 10, and 3 and 4, corresponded to the internally duplicated region on rice chromosomes 11 and 12 and suggested that this duplication in the rice genome predated the divergence of the Panicoideae and Oryzoideae subfamilies. Charting of the macroevolutionary steps leading to the modern maize genome clarifies the interpretation of intercladal comparative maps and facilitates alignments and genomic cross-referencing of genes and phenotypes among grass family members.

Chromosome Aberrations↗
PubMed1991

A comparison of intramolecular rearrangements promoted by transposons Tn5 and Tn10.

The bacterial transposon Tn10 has previously been shown to move to other genomic sites by a conservative mechanism, whereby the transposon is excised by double-strand breaks and inserted between a pair of staggered nicks at the target. Other transposons, like Tn3, have been shown to transpose by a replicative mechanism that involves symmetrical nicking of the element and formation of the 'Shapiro intermediate', which can mature into either a cointegrate or a simple insert. The situation with respect to Tn5 is unclear; it was originally reported to use a conservative mechanism, but other evidence suggests that the mechanism might be replicative. In this paper, rearrangements of adjacent DNA promoted by Tn10 and Tn5 have been compared using positive selection for galactose-resistance to detect such rearrangements. Tn10 promoted the formation of adjacent deletions (that started from an inside end of Tn10), deletion/inversions and simple IS10 insertions, but no cointegrates. This behaviour is fully consistent with a conservative mechanism. In contrast, Tn5 was found to promote formation of adjacent deletions (that started mainly from an outside end of Tn5), IS50 insertions (that were frequently accompanied by inversions of adjacent DNA) and cointegrates. These characteristics seem compatible with a replicative, rather than a conservative, mode of transposition. Clearly, Tn5 and Tn10 exhibit some significant differences in their transposition. These results, and results of some previous experiments, have been interpreted to mean that Tn5 could use a replicative mechanism for its transposition.

Base Sequence↗
PubMed1998

Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?

Extremely halophilic archaea, which flourish in hypersaline environments, are known to contain a variety of large dynamic replicons. Previously, the analysis of one such replicon, pNRC100, in Halobacterium sp. strain NRC-1, showed that it undergoes high-frequency insertion sequence (IS) element-mediated insertions and deletions, as well as inversions via recombination between 39-kb-long inverted repeats (IRs). Now, the complete sequencing of pNRC100, a 191,346-bp circle, has shown the presence of 27 IS elements representing eight families. A total of 176 ORFs or likely genes of 850-bp average size were found, 39 of which were repeated within the large IRs. More than one-half of the ORFs are likely to represent novel genes that have no known homologs in the databases. Among ORFs with previously characterized homologs, three different copies of putative plasmid replication and four copies of partitioning genes were found, suggesting that pNRC100 evolved from IS element-mediated fusions of several smaller plasmids. Consistent with this idea, putative genes typically found on plasmids, including those encoding a restriction-modification system and arsenic resistance, as well as buoyant gas-filled vesicles and a two-component regulatory system, were found on pNRC100. However, additional putative genes not expected on an extrachromosomal element, such as those encoding an electron transport chain cytochrome d oxidase, DNA nucleotide synthesis enzymes thioredoxin and thioredoxin reductase, and eukaryotic-like TATA-binding protein transcription factors and a chromosomal replication initiator protein were also found. A multi-step IS element-mediated process is proposed to account for the acquisition of these chromosomal genes. The finding of essential genes on pNRC100 and its property of resistance to curing suggest that this replicon may be evolving into a new chromosome.

Chromosome Mapping↗
PubMed1984

Effects of Ty insertions on HIS4 transcription in Saccharomyces cerevisiae.

Insertion of two different Ty elements into the Saccharomyces cerevisiae HIS4 regulatory region eliminates transcription of HIS4. Transcription can be restored by genetic rearrangements involving the Ty element inserted at HIS4. Several deletions, an inversion, a translocation, and a gene conversion are capable of restoring HIS4 transcription. Some of the rearrangements result in new transcriptional initiation sites. One type of revertant of his4-912 results from recombination between the delta elements flanking the Ty element, leaving a solo delta in place of the complete Ty. Strains carrying a Ty912 delta at HIS4 are His- at 23 degrees C. Unlinked suppressors (SPT) lead to suppression of this His- phenotype and increase levels of the normal HIS4 transcript. These suppressor genes affect not only the amount of transcription from the normal HIS4 initiation site, but also that from new initiation sites within Ty sequences adjacent to HIS4.

Alleles↗