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PubMed2003

Accurate analysis of power coupling between two arbitrarily ended dielectric slab waveguides by the boundary-element method.

The boundary integral equations that are called guided-mode extracted integral equations are applied to the investigation of the power-coupling-properties between two arbitrarily ended dielectric slab waveguides. The integral equations derived in this paper can be solved by the conventional boundary-element method. The reflection and coupling coefficients of the guided wave, as well as the scattering power, are calculated numerically for the case of incident TE guided-mode waves. The results presented are checked by the energy conservation law and the reciprocity theorem. Numerical results are presented for several geometries of coupling, including systems with three-layered symmetrical and asymmetrical slab waveguides.

Journal Article↗
PubMed1995

T-DNA integrations in a new family of repetitive elements of Nicotiana tabacum.

A number of T-DNA insertions in the genome of Nicotiana tabacum were characterized. One class of integrations was found to have occurred in a new family of highly repetitive sequences. Three genomic regions (ecoA, ecoB, and ecoC) were isolated, all of which contain basic units of 180 bp, organized in direct tandem repeats. Several of the 180-bp elements contain an EcoRI recognition site within the repeating unit and are therefore named "eco repeats." All members of this family are weakly homologous in sequence to a previously described class of repeat elements which contained a BamHI site (HRS60 repeat family), which suggests that both groups of sequences are of common evolutionary origin. The allotetraploid genome of N. tabacum is presumed to originate from the hybridization of two diploid genomes. The HRS60 elements previously described have been found exclusively in the genome of one of the ancestors, N. sylvestris, and in N. tabacum itself. Our DNA hybridization data suggest that the eco elements originate from the genome of the other ancestor, N. tomentosiformis. Whereas the HRS60 elements are transcriptionally silent, at least some eco elements appear to be transcribed.

Base Sequence↗
PubMed2004

An Erythroid-Specific Chromatin Opening Element Increases β-Globin Gene Expression from Integrated Retroviral Gene Transfer Vectors.

Gene therapy strategies requiring long-term high-level expression from integrated genes are currently limited by inconsistent levels of expression. This may be observed as variegated, silenced or position-dependent gene expression. Each of these phenomena involve suppressive chromatin structures. We hypothesized that by actively conferring an open chromatin structure on integrated vectors would increase transgene expression. To test this idea we used a 100bp element from the β-globin locus control region (LCR) which is able to independently open local chromatin structure in erythroid tissues. This element includes binding sites for GATA-1, NF-E2, EKLF and Sp-1 and is evolutionarily conserved. We constructed a series of MSCV-based vectors containing the β-globin gene driven by a minimal β-globin promoter with combinations of the HSFE and LCR derived enhancer elements. Pools of MEL clones containing integrated vectors were analyzed for chromatin structure and β-globin gene expression. The HSFE increased the extent of nuclease sensitive chromatin over the promoters of the constructs. The most effective vector included tandem copies of the HSFE and produced a 5-fold increase in expression compared to the promoter alone. These results indicate that the HSFE is able to augment the opening of β-globin promoter chromatin structure and significantly increase gene expression in the context of an integrated retroviral vector.

Journal Article↗
PubMed1997

Genomic structure and evolution of a novel gene (PLA2L) with duplicated phospholipase A2-like domains.

In a previous study, we isolated a novel human cDNA with two domains of homology to secreted phospholipase A2 (sPLA2) embedded within a much larger open reading frame. The corresponding gene, termed PLA2L, is also unusual in that it is transcribed from an endogenous retroviral long terminal repeat promoter in teratocarcinoma cell lines. The associated retroviral element, a member of the HERV-H family of sequences, is found within an intron of the human PLA2L gene and has apparently assumed transcriptional regulatory functions at this locus. In this study we have isolated genomic clones spanning the human PLA2L locus and have determined the intron/exon structure of the PLA2-like domains. This intron/exon structure is very similar to that of known sPLA2s despite the fact that the PLA2L gene is highly diverged and has a novel duplicated structure. We also mapped PLA2L to chromosome 8q24, a location that differs from the known locations of human sPLA2s. Genomic PCR across primate species was performed to determine the approximate time of integration of the HERV-H element. Results indicate that the element integrated 15-20 million years ago since it is present in chimpanzee and gorilla but absent in orangutan and lower primates. Although the function of the PLA2L gene is not known, genomic Southern analyses suggest evolutionary conservation in mammals. These results contribute to our understanding of the unique and complex evolutionary history of the PLA2L gene.

Amino Acid Sequence↗
PubMed1997

Comparative analyses of LTRs of the ERV-H family of primate-specific retrovirus-like elements isolated from marmoset, African green monkey, and man.

We have isolated 8 different long terminal repeat (LTR) sequences of the ERV-H family of endogenous retrovirus-like elements from human chromosome 18, 9 from African green monkey, and 28 from marmoset. Human ERV-H LTRs have been divided into three types designated Type I, Type Ia, and Type II. Comparative analyses of the 45 isolated LTRs and 60 human ERV-H LTRs enabled a further subdivision into 13 subtypes. Type I elements were widely distributed in all three species. Their average evolutionary age (40 MYr), estimated by a consensus sequence approach, suggests that they first expanded in the genomes at the time New- and Old World monkeys diverged. The occurence of some very old Type I sequences indicate that ERV-H elements may have integrated even before prosimians and primates diverged. Type Ia and - II elements were found in both monkey species. Promoter active Type I and Type Ia LTRs were found while Type II LTRs were inactive. Promoter active Type I LTRs generally contained a functional GC/GT box immediately 3' to the TATA box, providing strong binding of Sp1 family proteins, while the highly promoter active Type Ia element H6 contained synergistically acting Sp1 binding sites located in the U3 enhancer region.

Animals↗
PubMed1994

A self-stabilizing Ac derivative and its potential for transposon tagging.

With the goal of developing a self-stabilizing transposon tagging system, a derivative of the maize transposable element Ac (Ds303) harbouring a deletion between bp 246 and 736 has been introduced into tomato (Lycopersicon esculentum) by Agrobacterium tumefaciens-mediated transformation. The deletion removes the major transcription start site, 84 bp of the putative Ac promoter and part of the untranslated leader. Transpositions from the T-DNA, where Ds303 was inserted between the mannopine synthase 1' promoter and the GUS gene, were observed in four independent transgenic plants analysed. After transposition the transposed Ds303 elements were stably integrated in the genome and could not transactivate a tester Ds element. However, somatic and germinal transpositions of the transposed Ds303 elements occurred in the presence of a transposase source.

Base Sequence↗
PubMed2006

Requirement for Vibrio cholerae integration host factor in conjugative DNA transfer.

The requirement for host factors in the transmission of integrative and conjugative elements (ICEs) has not been extensively explored. Here we tested whether integration host factor (IHF) or Fis, two host-encoded nucleoid proteins, are required for transfer of SXT, a Vibrio cholerae-derived ICE that can be transmitted to many gram-negative species. Fis did not influence the transfer of SXT to or from V. cholerae. In contrast, IHF proved to be required for V. cholerae to act as an SXT donor. In the absence of IHF, V. cholerae displayed a modest defect for serving as an SXT recipient. Surprisingly, SXT integration into or excision from the V. cholerae chromosome, which requires an SXT-encoded integrase related to lambda integrase, did not require IHF. Therefore, the defect in SXT transmission in the V. cholerae IHF mutant is probably not related to IHF's ability to promote DNA recombination. The V. cholerae IHF mutant was also highly impaired as a donor of RP4, a broad-host-range conjugative plasmid. Thus, the V. cholerae IHF mutant appears to have a general defect in conjugation. Escherichia coli IHF mutants were not impaired as donors or recipients of SXT or RP4, indicating that IHF is a V. cholerae-specific conjugation factor.

Bacterial Proteins↗
PubMed2005

Recommendations for comprehensive stroke centers: a consensus statement from the Brain Attack Coalition.

BACKGROUND AND PURPOSE: To develop recommendations for the establishment of comprehensive stroke centers capable of delivering the full spectrum of care to seriously ill patients with stroke and cerebrovascular disease. Recommendations were developed by members of the Brain Attack Coalition (BAC), which is a multidisciplinary group of members from major professional organizations involved with the care of patients with stroke and cerebrovascular disease. SUMMARY OF REVIEW: A comprehensive literature search was conducted from 1966 through December 2004 using Medline and Pub Med. Articles with information about clinical trials, meta-analyses, care guidelines, scientific guidelines, and other relevant clinical and research reports were examined and graded using established evidence-based medicine approaches for therapeutic and diagnostic modalities. Evidence was also obtained from a questionnaire survey sent to leaders in cerebrovascular disease. Members of BAC reviewed literature related to their field and graded the scientific evidence on the various diagnostic and treatment modalities for stroke. Input was obtained from the organizations represented by BAC. BAC met on several occasions to review each specific recommendation and reach a consensus about its importance in light of other medical, logistical, and financial factors. CONCLUSIONS: There are a number of key areas supported by evidence-based medicine that are important for a comprehensive stroke center and its ability to deliver the wide variety of specialized care needed by patients with serious cerebrovascular disease. These areas include: (1) health care personnel with specific expertise in a number of disciplines, including neurosurgery and vascular neurology; (2) advanced neuroimaging capabilities such as MRI and various types of cerebral angiography; (3) surgical and endovascular techniques, including clipping and coiling of intracranial aneurysms, carotid endarterectomy, and intra-arterial thrombolytic therapy; and (4) other specific infrastructure and programmatic elements such as an intensive care unit and a stroke registry. Integration of these elements into a coordinated hospital-based program or system is likely to improve outcomes of patients with strokes and complex cerebrovascular disease who require the services of a comprehensive stroke center.

Academic Medical Centers↗
PubMed2005

Integrating child health information systems.

The Health Resources and Services Administration and All Kids Count (a national technical assistance center fostering development of integrated child health information systems) have been working together to foster development of integrated child health information systems. Activities have included: identification of key elements for successful integration of systems; development of principles and core functions for the systems; a survey of state and local integration efforts; and a conference to develop a common vision for child health information systems to meet medical care and public health needs. We provide 1 state (Utah) as an example that is well on the way to development of integrated child health information systems.

Child↗
PubMed1995

Bacterial transposases and retroviral integrases.

Transposable genetic elements have adopted two major strategies for their displacement from one site to another within and between genomes. One involves passage through an RNA intermediate prior to synthesis of a DNA copy while the other is limited uniquely to DNA intermediates. For both types of element, recombination reactions involved in integration are carried out by element-specific enzymes. These are called transposases in the case of DNA elements and integrases in the case of the best-characterized RNA elements, the retroviruses and retrotransposons. In spite of major differences between these two transposition strategies, one step in the process, that of insertion, appears to be chemically identical. Current evidence suggests that the similarities in integration mechanism are reflected in amino acid sequence similarities between the integrases and many transposases. These similarities are particularly marked in a region which is thought to form part of the active site, namely the DDE motif. In the light of these relationships, we attempt here to compare mechanistic aspects of retroviral integration with transposition of DNA elements and to summarize current understanding of the functional organization of integrases and transposases.

Amino Acid Sequence↗
PubMed1997

Analysis of sequences flanking the vap regions of Dichelobacter nodosus: evidence for multiple integration events, a killer system, and a new genetic element.

Dichelobacter nodosus is the causative agent of ovine footrot. The vap regions of the D. nodosus genome may have arisen by the integration of a genetic element and may have a role in virulence. The virulent D. nodosus strain A198 has multiple copies of the vap regions. In the present study, sequences to the left and right of vap regions 1, 2 and 3 of strain A198 were analysed by Southern blotting and DNa sequencing. The results suggest that vap regions 1 and 2 rose by independent integration events into different tRNA genes. The discovery of a second integrase gene (intB), a gene with similarity to bacteriophage repressor proteins (regA), and a gene similar to an ORF from a conjugative transposon (gepA), suggests that a second genetic element, either a bacteriophage or a conjugative transposon, is integrated next to vap region 3 in the D. nodosus genome. The arrangement of intB and the vap regions in three other virulent strains and one benign strain was determined using using Southern blotting and PCR. One strain, H1215, contained vapE' and not vapE, and thus resembles vap region 3, suggesting that vap region 3 also may have arisen by an independent integration event. In all strains, a copy of intB was found next to the vap regions. The vap regions contain two genes, vapA and toxA, with similarity to the hig genes of the killer plasmid Rts1. Evidence is presented that vapA and toxA have a similar function in D. nodosus.

Amino Acid Sequence↗
PubMed1997

Detection and cloning of unique integration sites of retrotransposon, intracisternal A-particle element in the genome of acute myeloid leukemia cells in mice.

We previously found retrotransposition of the intracisternal A-particle (IAP) element in the genome of acute myeloid leukemia (AML) cells induced by X-irradiation of C3H/He mice (FEBS 16333). To analyze the occurrence of the IAP-mediated retrotransposition in AML cells, we compared integration sites of the IAP element by polymerase chain reaction (PCR) in the genomes of five AML strains derived from different C3H mice. Unique PCR products were found in all of the above independent leukemia cells, whereas no such products were detected in normal cells. Results of cloning, sequencing and Southern analyses showed that the PCR products were derived from novel integration sites of the IAP element in the genome. The data suggest that IAP-mediated retrotransposition occurs frequently in radiation-induced AML cells from C3H/He mice.

Animals↗
PubMed1983

The normal developmental regulation of a cloned sgs3 'glue' gene chromosomally integrated in Drosophila melanogaster by P element transformation.

A 7-kb genomic segment containing the coding sequence for the Drosophila melanogaster Formosa variant of salivary gland secretion protein 3 (sgs3) has been inserted into the snw y, bw, st strain of D. melanogaster using the P transformation vector p.6.1. The inserted sequence codes for a shorter RNA which can be distinguished from that of the host gene. The amount of RNA, and its stage- and tissue-specific synthesis is identical to that of the host gene, which suggests that all the cis-acting regulatory DNA sequences for this gene are contained within this 7-kb segment.

Animals↗
PubMed1985

Transposition in plants: a molecular model.

A molecular model for transposition of plant transposable elements is described. This process may occur via excision and re-integration of the element. Excision generates DNA sequence diversity which suggests the participation of DNA repair enzymes in the healing of the donor molecule.

DNA Transposable Elements↗
PubMedDate not supplied

The Ecological Areawide Management (TEAM) of leafy spurge program of the United States Department of Agriculture-Agricultural Research Service.

The Ecological Areawide Management (TEAM) of Leafy Spurge program was developed to focus research and control efforts on a single weed, leafy spurge, and demonstrate the effectiveness of a coordinated, biologically based, integrated pest management program (IPM). This was accomplished through partnerships and teamwork that clearly demonstrated the advantages of the biologically based IPM approach. However, the success of regional weed control programs horizontally across several states and provinces also requires a vertical integration of several sectors of society. Awareness and education are the essential elements of vertical integration. Therefore, a substantial effort was made to produce a wide variety of information products specifically designed to educate different segments of society. During its tenure, land managers and agency decision makers have seen the potential of using the TEAM approach to accelerate the regional control of leafy spurge. The example set by the TEAM organization and participants is viewed as a model for future weed-control efforts.

Agriculture↗
PubMed1995

Design optimization of the hip nail-plate-screws implant.

This paper is aimed at determining the number of screws and the dimensions of the appliance components of a hip nail-plate screw implant such that their sizes are a minimum (i.e. the implant weight is minimum), without the stresses in the appliance components as well as in the bone shaft exceeding the allowable limits. The implant-bone structure is idealized as a hybrid frame, composed of appliance components and the supporting femur bone elements, which act integrally to support the maximal load (during the gait cycle) at the hip joint. For various configurations of the implant, entailing different numbers of screws, the optimization technique is employed to determine the size of the members (nail, plate and screws) for a lightweight design. Implant configurations are analyzed for two, three, four and five nail configurations. The analysis of the hybrid (implant femur) frame, during each integrative object function and design parameter evaluation, is done by the Finite Element Method. The optimization problem is solved by the sequential unconstrained minimization technique (with the introduction of interior penalty function terms). It is found, from the results of analyses of the four hybrid frames, that the appliance frame, with two screws, yields the minimum-weight structurally safe design.

Biomechanical Phenomena↗
PubMed1997

Complete conversion of antibiotic precursor to pristinamycin IIA by overexpression of Streptomyces pristinaespiralis biosynthetic genes.

A Streptomyces pristinaespiralis strain, which produces a streptogramin antibiotic pristinamycin II (PII) as a mixture of two biologically active molecules PIIB and PIIA, was genetically engineered to produce exclusively PIIA. The snaA,B genes, which encode a PIIA synthase that performs oxidation of the precursor (PIIB) to the final product (PIIA), were integrated in the chromosome of S. pristinaespiralis using an integrative derivative of the pSAM2 genetic element from Streptomyces ambofaciens. Integration was due to site-specific recombination at the attB site of S. pristinaespiralis, and no homologous recombination at the snaA,B locus was observed. The attB site of S. pristinaespiralis was sequenced and found to overlap the 3' end of a pro-tRNA gene. The integrants were stable in industrial conditions of pristinamycin production and showed no decrease in PII biosynthesis. Western blot analysis showed a constant production of the PIIA synthase in the overall fermentation process due to expression of the cloned snaA,B genes from the constitutive ermE promoter. This allows the complete conversion of the PIIB form into PIIA.

Attachment Sites, Microbiological↗