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PubMed1999

Distribution and evolution of mobile elements in the virilis species group of Drosophila.

The distributions of Penelope and Ulysses, two transposable elements that can induce hybrid dysgenesis, were studied in several species groups of Drosophila. No significant hybridization to Penelope and Ulysses probes was detected by Southern blot analyses of species outside the virilis group. In contrast, both element families have had a long residence in all species of the virilis species group, as indicated by their strong presence in the heterochromatic chromocenter. Except for D. kanekoi, D. lummei, and some strains of D. virilis, species of the group carry full-sized, and at least potentially functional, copies of both element families. Consistent with the occurrence of recent transposition, Penelope and Ulysses elements are located at different chromosomal sites in different geographical strains of the same species. A total of 79 Penelope and 47 Ulysses euchromatic insertion sites were localized to chromosomal subsections in species of the virilis group. Highly significant deviations from independence of the distributions of Penelope and Ulysses and previously established inversion breakpoints were documented, suggesting that these transposable elements may have played an important role in genomic reorganization and evolution of the virilis species group, which is especially rich in karyotypic variation.

Animals↗

PubMed1995

Intraoperative optimization of needle placement and dwell times for conformal prostate brachytherapy.

PURPOSE: Traditionally, transperineal prostate brachytherapy has been heavily operator dependent. To overcome this limitation, a treatment planning method was developed for intraoperative planning, guidance, and evaluation. In this setting, reliability, speed, and ease of understanding are primary considerations. This planning method has been implemented for ultrasound guided implants of the prostate, but can be extended for use in other body sites. METHODS AND MATERIALS: The length and cross-section of the target (prostate) and location of urethra and rectum are determined intraoperatively from live ultrasound imaging. The planning program then automatically generates a "reference plan" containing needle locations, dwell times, and the resulting isodose distribution. As needles are placed, this information is corrected to account for any deviation of needle placement or movement of the prostate. Once all needles are in place, the normalization is adjusted to reconcile remaining hot-spots with coverage of the target volume. Optimization is performed in three separate stages. Each stage works to enhance only a subset of the implant parameters. (a) Pattern Optimization attempts to find the most appropriate placement for the needles or catheters. It is based on the transverse contour of the target volume. Needles are placed uniformly around the perimeter, and interior needle positions are determined from the cross-sectional area and shape. Critical structures such as the urethra are explicitly avoided. This step provides the overall framework for the implant, and is not generally repeated. (b) Relative Dwell Time Optimization selects relative dwell times that will give the best uniformity of dose. It works by setting the relative dwell time in each source position inversely proportional to the dose delivered to that point by the other source positions. It is used in the reference plan, and is repeated as each needle is inserted. This provides dosimetric feedback to the physician, who can judge the effect of deviations from the reference plan. (c) Relative Volume Optimization is an interactive method for fine tuning the normalization based upon volume analysis. The volume analysis is presented in tabular and graphical form, both being updated rapidly as the normalization is adjusted. The information is formatted to help the operator judge coverage and uniformity. Special functions are provided that allow the operator to "jump" to special normalization values based on several indices of uniformity or uniformity/coverage. RESULTS: This system overcomes some conventional brachytherapy limitations. Rather than depend on the operator's intuitive judgement of where the needles should be placed, a global plan is generated and validated with full dose calculations. Immediate feedback is provided concerning the adequacy of placement and avoidance of critical structures. This information is provided in terms of actual tissue doses to the target volume and critical structures using point doses, isodose distributions, and volume analysis. Since the new method was introduced in January 1994, 33 implants have been performed. The needle placement method has been reliable in the clinic, with different doctors producing similar results on subsequent fractions for the same patient. CONCLUSION: The method of decomposing the optimization problem into several simple steps is capable of rapidly, consistently, and reliably designing conformal treatment plans of high uniformity. Operator dependence has been significantly reduced. We are adapting the method for other anatomic sites.

Brachytherapy↗

PubMed2006

Transposon mutagenesis of Bacillus anthracis strain Sterne using Bursa aurealis.

Bacillus anthracis, a spore forming Gram-positive microbe, is the causative agent of anthrax. Although plasmid encoded factors such as lethal toxin (LeTx), edema toxin (EdTx), and gamma-poly-d-glutamic acid (PGA) capsule are known to be required for disease pathogenesis, B. anthracis genes that enable spore invasion, phagosomal escape and macrophage replication are still unknown. To establish transposon mutagenesis as a tool for the characterization of anthrax genes, we employed the mariner-based mini-transposon Bursa aurealis in B. anthracis strain Sterne 7702. B. aurealis carrying an erythromycin resistance cassette and its cognate transposase were delivered by transformation of two plasmids. B. aurealis transposition can be selected for by temperature shift to prevent plasmid replication and by screening colonies for erythromycin resistance. Using inverse polymerase chain reaction, DNA fragments of 129 random erythromycin-resistant transposon mutants were amplified and submitted to DNA sequence analysis. These studies demonstrate that B. aurealis inserts randomly into the genome of B. anthracis and can therefore be employed for finding genes involved in virulence.

Antigens, Bacterial↗

PubMed2001

The porcine gonadotropin-releasing hormone receptor gene (GNRHR): genomic organization, polymorphisms, and association with the number of corpora lutea.

The interaction of gonadotropin-releasing hormone (GNRH) and its receptor (GNRHR) is critical in the endocrine regulation of reproduction. The gene (GNRHR) encoding the receptor has been mapped to porcine chromosome 8. There is evidence for three quantitative trait loci (QTL) influencing ovulation rate on this chromosome. We obtained an almost complete sequence (3993 bp, excluding intron 1) of the porcine GNRHR gene using PCR-based comparative genomic walking and inverse genomic walking approaches. Twelve polymorphisms were detected by sequencing of pooled DNA of Chinese Taihu and European Large White pigs, including 7 base substitutions and 5 insertions-deletions (indels). A F2 population of Meishan x European Large White pigs was genotyped for a TG indel in the promoter region, and a C/G substitution in the 3' UTR (untranslated region). A significant association of the C/G substitution with number of corpora lutea at first parity was observed.

3' Untranslated Regions↗

PubMed1996

A method to invert DNA segments of the Bacillus subtilis 168 genome by recombination between two homologous sequences.

We developed a method that allows rapid isolation of mutant Bacillus subtilis 168 carrying an inversion of a specific DNA segment of the genome. Two incomplete neomycin resistance gene cassettes were integrated at both ends of the 1652-kb segment to be inverted. Reciprocal recombination within the 590-bp homologous region of these two cassettes created an intact neomycin resistance gene with concomitant inversion of the 1652-kb segment flanked by the two cassettes. Structure of the mutant genome was verified by analyzing the physical map for rare cutting endonucleases, SfiI, NotI, I-CeuI, and I-SceI. The inversion rate was estimated to be 6.9 +/- 1.4 x 10(-8)/cell/cell division at 37 degrees C. The method should be in principle applicable not only to other regions of the B, subtilis genome but also to other bacterial genomes.

Anti-Bacterial Agents↗

PubMed2006

V(D)J recombinase-mediated processing of coding junctions at cryptic recombination signal sequences in peripheral T cells during human development.

V(D)J recombinase mediates rearrangements at immune loci and cryptic recombination signal sequences (cRSS), resulting in a variety of genomic rearrangements in normal lymphocytes and leukemic cells from children and adults. The frequency at which these rearrangements occur and their potential pathologic consequences are developmentally dependent. To gain insight into V(D)J recombinase-mediated events during human development, we investigated 265 coding junctions associated with cRSS sites at the hypoxanthine-guanine phosphoribosyltransferase (HPRT) locus in peripheral T cells from 111 children during the late stages of fetal development through early adolescence. We observed a number of specific V(D)J recombinase processing features that were both age and gender dependent. In particular, TdT-mediated nucleotide insertions varied depending on age and gender, including percentage of coding junctions containing N-nucleotide inserts, predominance of GC nucleotides, and presence of inverted repeats (Pr-nucleotides) at processed coding ends. In addition, the extent of exonucleolytic processing of coding ends was inversely related to age. We also observed a coding-partner-dependent difference in exonucleolytic processing and an age-specific difference in the subtypes of V(D)J-mediated events. We investigated these age- and gender-specific differences with recombination signal information content analysis of the cRSS sites in the human HPRT locus to gain insight into the mechanisms mediating these developmentally specific V(D)J recombinase-mediated rearrangements in humans.

Adolescent↗

PubMed2002

Prenatal diagnosis of a de novo inversion of chromosome (2)(p21q11).

Prenatal diagnosis of "apparently balanced" chromosomal rearrangements, if not inherited from a parent, are problematic for genetic counsellors and families. Although the parents need to be informed about the increased risk of multiple congenital anomalies, the anomalies that the fetus is at risk can not be discussed unless a similar breakpoint and accompanying phenotype have been reported in the literature. In the reported case prenatal ultrasound examination revealed a massive hydrocephalus internus and IUGR. The karyotype of the fetus was inv(2)(p21q11) de novo. Postmortem examination revealed short palpebral fissures, hypertelorism, atypical nasiolabial configuration, microgenia, extended position of the fingers, atypical proximal inserted first toe, hydrocephalus internus, hypoplasia of the cerebellum and bulbi olfactorii, bilateral hypoplastic lungs, atrial septal defect II, small right ventricle, dysplasia of the pulmonary valve, hypoplastic pulmonary artery, right proximal ureterostenosis, hypoplastic gall bladder. This is the first description of a de novo inversion (2)(p21q11) in a fetus with multiple malformations.

Abnormalities, Multiple↗

PubMed1983

Biosynthesis of the photosynthetic membranes of Rhodopseudomonas sphaeroides.

The steady-state biosynthesis of the photosynthetic membrane (ICM) of Rhodopseudomonas sphaeroides has been reviewed. At moderate light intensities, 500 ft-c, preexisting ICM serves as the insertion matrix for newly synthesized membrane components. Whereas the bulk of the membrane protein, protein-pigment complexes, and pigments are inserted into preexisting ICM throughout the cell cycle, phospholipid is transferred from outside the ICM to the ICM only at the time of cell division. Because the site of cellular phospholipid synthesis is the cytoplasmic membrane, these results infer that despite the physical continuity of cytoplasmic membrane and ICM, there must exist between these membranous domains a "barrier" to the free diffusion of cellular phospholipid. The cyclical alternation in protein to phospholipid ratio of the ICM infers major structural and functional alternations, such as changes in the protein to lipid ratio of the membrane, specific density of the membrane, lipid structure within the membrane, and the rate of cyclic electron flow. When biochemical studies are correlated with detailed electron microscopic investigations we can further conclude that the number of photosynthetic units within the plane of the membrane can vary by nearly a factor of two over the course of the cell cycle. The average physical size of the photosynthetic units is constant for a given light intensity but inversely proportional to light intensity. The distribution of photosynthetic unit size classes within the membrane can be interpreted as suggesting that the "core" of the photosynthetic unit (reaction center plus fixed antenna complex) is inserted into the membrane coordinately as a structural entity. The variable antenna complex is, on the other hand, inserted independent of the "core" and randomly associates with both old and new core complexes. Finally, we conclude that there is substantial substructure to te distribution of photosynthetic units within the ICM, ie, they are highly ordered and exist in a defined spatial orientation to one another.

Bacterial Chromatophores↗

PubMed1990

Chromosome engineering in Saccharomyces cerevisiae by using a site-specific recombination system of a yeast plasmid.

We have developed an effective method to delete or invert a chromosomal segment and to create reciprocal recombination between two nonhomologous chromosomes in Saccharomyces cerevisiae, using the site-specific recombination system of pSR1, a circular cryptic DNA plasmid resembling 2 microns DNA of S. cerevisiae but originating from another yeast, Zygosaccharomyces rouxii. A 2.1-kilobase-pair DNA fragment bearing the specific recombination site on the inverted repeats of pSR1 was inserted at target sites on a single or two different chromosomes of S. cerevisiae by using integrative vectors. The cells were then transformed with a plasmid bearing the R gene of pSR1, which encodes the site-specific recombination enzyme and is placed downstream of the GAL1 promoter. When the transformants were cultivated in galactose medium, the recombination enzyme produced by expression of the R gene created the modified chromosome(s) by recombination between two specific recombination sites inserted on the chromosome(s).

Base Sequence↗

PubMed1993

Macroevolution by transposition: drastic modification of DNA recognition by a type I restriction enzyme following Tn5 transposition.

We have characterized a novel mutant of EcoDXXI, a type IC DNA restriction and modification (R-M) system, in which the specificity has been altered due to a Tn5 insertion into the middle of hsdS, the gene which encodes the polypeptide that confers DNA sequence specificity to both the restriction and the modification reactions. Like other type I enzymes, the wild type EcoDXXI recognizes a sequence composed of two asymmetrical half sites separated by a spacer region: TCA(N7)RTTC. Purification of the EcoDXXI mutant methylase and subsequent in vitro DNA methylation assays identified the mutant recognition sequence as an interrupted palindrome, TCA(N8)TGA, in which the 5' half site of the wild type site is repeated in inverse orientation. The additional base pair in the non-specific spacer of the mutant recognition sequence maintains the proper spacing between the two methylatable adenine groups. Sequencing of both the wild type and mutant EcoDXXI hsdS genes showed that the Tn5 insertion occurred at nucleotide 673 of the 1221 bp gene. This effectively deletes the entire carboxyl-terminal DNA binding domain which recognizes the 3' half of the EcoDXXI binding site. The truncated hsdS gene still encodes both the amino-terminal DNA binding domain and the conserved repeated sequence that defines the length of the recognition site spacer region. We propose that the EcoDXXI mutant methylase utilizes two truncated hsdS subunits to recognize its binding site. The implications of this finding in terms of subunit interactions and the malleability of the type I R-M systems will be discussed.

Base Sequence↗

PubMed2001

Complex cytogenetic rearrangement of chromosome 8q in a case of Ambras syndrome.

Ambras syndrome (AMS) is a unique form of congenital universal hypertrichosis. The syndrome has been found in association with rearrangements of chromosome 8 in two isolated cases. One of these patients was reported to have an apparently balanced paracentric inversion of chromosome 8, inv(8)(q12q22). Our cytogenetic analysis on this patient showed that the rearrangement of chromosome 8 is more complex than initially reported. We detected an insertion of the q23-q24 region into a more proximal region of the long arm of chromosome 8 as well as a large deletion in 8q23:46,XX, rea(8)(8pter-->8q13::8q23.2-->8q24.1::8q13-->8q23.1::8q24.1-->8qter). Given the large number of breakpoints and the presence of a substantial deletion, it is surprising that the proposita did not show anomalies other than these characteristic of Ambras syndrome.

Child, Preschool↗

PubMed1997

Identification of a homolog of the C alpha 3'/hs3 enhancer and of an allelic variant of the 3'IgH/hs1,2 enhancer downstream of the human immunoglobulin alpha 1 gene.

Although four regulatory elements are known downstream of the mouse IgH alpha gene, a single enhancer homologous to hs1,2 has been thus far described downstream of each human alpha gene (Chen, C. and Birshtein, B. K., J. Immunol. 1997. 159: 1310). We characterized a 10-kb region downstream of the human alpha 1 gene. Two B cell-specific regulatory elements homologous to the murine C alpha 3'/hs3 and hs1,2,3' enhancers were found, which are duplicated downstream of alpha 2. The hs1,2 element is in inverted orientation by comparison with a recently reported alpha 1 hs1,2 element: it appears as a common allelic variant carrying an internal tandem repeat insertion and its prevalence in the human population is 60%. As in the mouse, the human hs1,2 enhancer is flanked with long inverted repeats which may have promoted inversion events through homologous recombination. Although the palindromic organization of the region is maintained in human, sequence identity with rodents focuses on core enhancer elements rather than on flanking repeats. Concerted divergence of both sides of the dyad symmetry suggests that inverted repeats are not just evolutionary remnants but rather play an architectural role in the LCR function.

Alleles↗

PubMedDate not supplied

Serum albumin.

The liver manufactures albumin at a massive rate and decreases production in times of environmental, nutritional, toxic and trauma stress. Osmotic pressure is a basic evolutionary regulatory factor, and hormonal control over albumin production has been demonstrated. Where and why new or old albumin is degraded are questions which have not been clarified, although the vascular endothelium may well be the degradative site. Albumin is important as a transport protein, as a measure of evolution and as a model to study secretion following synthesis without the intervening steps of glycosylation. Investigations as to how this protein enters the endoplasmic membrane may well answer some of the questions concerning signal peptide insertion (288). The role of the urea cycle intermediate ornithine and its participation in polyamine synthesis, which has a positive effect on albumin synthesis, is under study. Likewise, the inverse relation between acute-phase protein synthesis and albumin synthesis regulated by interleukin 1 and other cytokines will merit further study. These are a few of the concepts which will be tested in the future.

Aging↗

PubMed1992

A general method for chimerization of monoclonal antibodies by inverse polymerase chain reaction which conserves authentic N-terminal sequences.

Chimerization of antibodies (Ab) by cloning the V (variable) regions encoding the light and heavy chains with degenerate oligodeoxyribonucleotide primers matching to framework region 1 and to the joining regions, leads to Ab with altered amino acids at the N-terminus compared to those of the parental Ab. This is due to N-terminal framework 1 sequences in the expression vectors [Larrick et al., Bio/Technology 7 (1989) 937-938; Le Boeuf et al., Gene (1989) 371-377; Orlandi et al., Proc. Natl. Acad. Sci. USA 86 (1989) 3833-3837]. This might lead to Ab with altered affinity to the antigen due to interaction of framework sequences with complementarity determining regions. Moreover, some V regions may be refractory to cloning by this procedure. Here, we describe a method to circumvent these potential problems. The V regions for both chains of the Ab are cloned by inverse polymerase chain reaction (PCR) with primers matching the known constant region sequences of the Ab. After sequencing, PCR fragments corresponding to the V regions of both chains are inserted in-frame into appropriate expression vectors leading to Ab with unaltered N-terminal sequences after expression in mammalian cells. The procedure is illustrated with an Ab directed against the beta chain of the human interleukin-2 receptor.

Amino Acid Sequence↗

PubMed2004

Fluoride-promoted cross-coupling reactions of alkenylsilanols. Elucidation of the mechanism through spectroscopic and kinetic analysis.

The mechanism of the palladium-catalyzed cross-coupling reaction of (E)-dimethyl-(1-heptenyl)silanol ((E)-1) and of (E)-diisopropyl-(1-heptenyl)silanol ((E)-2) with 2-iodothiophene has been investigated through spectroscopic and kinetic analysis. A common intermediate in cross-coupling reactions of several types of organosilicon precursors has been identified as a hydrogen-bonded complex between tetrabutylammonium fluoride (TBAF) and a silanol. The order in each component has been determined by plotting the initial rates of the cross-coupling reaction at varying concentrations. These data provide a mechanistic picture that involves a fast and irreversible oxidative insertion of palladium into the aryl iodide and a subsequent turnover-limiting transmetalation step achieved through a fluoride-activated disiloxane derived from the particular silanol employed. The inverse order dependence of TBAF at high concentration is consistent with a pathway that proceeds through a hydrogen-bonded complex which is the lowest energy silicon species in solution.

Hydrogen Bonding↗

PubMed2003

The molecular basis of hemophilia A: genotype-phenotype relationships and inhibitor development.

The molecular basis of hemophilia A has been extensively studied over the last two decades, and this analysis of the factor VIII (FVIII) gene has rendered it one of the most studied of all human genes. A wide range of different mutation types has been identified that includes the novel intrachromosomal inversions involving regions in introns 1 and 22 of the FVIII gene as well as many mutation types found in other genetic diseases, including large and small deletions and insertions, and point mutations resulting in nonsense, missense, and splice site mutations. Inhibitory antibodies that develop in a proportion of patients with hemophilia A following replacement therapy are now known to correlate with FVIII mutation type and location. This correlation is demonstrated, and a potential algorithm for predicting inhibitor development in newly diagnosed patients is presented. Many patients with mild hemophilia A have a discrepancy between the levels of FVIII:C determined by the one-stage and two-stage assays. The molecular basis of the discrepancy is explored. This article thus highlights both the molecular basis of hemophilia and some of the additional information that can be gained from determination of the mutation responsible for hemophilia in affected patients.

Algorithms↗

PubMed1996

Isolation of the full-length murine erythropoietin receptor using a baculovirus expression system.

The full-length murine erythropoietin receptor was expressed in Spodoptera frugiperda (Sf9) cells using a recombinant baculovirus vector. Erythropoietin receptor protein production was maximal 48 hours after infection, as determined by metabolic labeling and immunoblotting; receptor protein varied in molecular mass from 62 to 76 kD. Erythropoietin receptors produced in Sf9 cells could be solubilized using CHAPS in a form capable of binding erythropoietin, and the solubilized receptor bound to immobilized Concanavalin A (Con A) and wheat germ agglutinin, as well as to immobilized recombinant human erythropoietin. Analysis of the distribution of erythropoietin receptors in Sf9 plasma membrane and cytosol fractions using lectin affinity chromatography revealed that membrane-bound receptor had a higher apparent molecular mass and contained the bulk of receptors that bound to wheat germ agglutinin. The receptor was purified by sequential affinity chromatography on Con A-Sepharose and immobilized erythropoietin. Erythropoietin receptors expressed in Sf9 cells were inserted into the plasma membrane in the correct orientation, bound 125I-erythropoietin with a single affinity (kD, 330 pmol/L), and were internalized after ligand binding. However, kD varied inversely with the number of cell surface receptors. Solubilized erythropoietin receptors in whole-cell lysates and isolated plasma membranes exhibited high-affinity binding, with kD values of 92 and 57 pmol/L, respectively. Erythropoietin bound to the surface of infected Sf9 cells could be cross-linked to two proteins with molecular masses of 90 and 65 kD using the homobifunctional cross-linker, disuccinimidyl suberate (DSS). Similar results were obtained with solubilized receptors in whole-cell lysates, and both proteins could be immunoprecipitated by an antiserum to the erythropoietin receptor carboxyl-terminal domain.

Animals↗

PubMed2004

Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae.

Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome sequence of R. typhi (1,111,496 bp) and compare it to the two published rickettsial genome sequences: R. prowazekii and R. conorii. We identified 877 genes in R. typhi encoding 3 rRNAs, 33 tRNAs, 3 noncoding RNAs, and 838 proteins, 3 of which are frameshifts. In addition, we discovered more than 40 pseudogenes, including the entire cytochrome c oxidase system. The three rickettsial genomes share 775 genes: 23 are found only in R. prowazekii and R. typhi, 15 are found only in R. conorii and R. typhi, and 24 are unique to R. typhi. Although most of the genes are colinear, there is a 35-kb inversion in gene order, which is close to the replication terminus, in R. typhi, compared to R. prowazekii and R. conorii. In addition, we found a 124-kb R. typhi-specific inversion, starting 19 kb from the origin of replication, compared to R. prowazekii and R. conorii. Inversions in this region are also seen in the unpublished genome sequences of R. sibirica and R. rickettsii, indicating that this region is a hot spot for rearrangements. Genome comparisons also revealed a 12-kb insertion in the R. prowazekii genome, relative to R. typhi and R. conorii, which appears to have occurred after the typhus (R. prowazekii and R. typhi) and spotted fever (R. conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae.

Chromosome Inversion↗