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PubMed2003

Monolithic integration of dual-layer optics into broad-area semiconductor laser diodes.

A broad-area semiconductor laser diode with two monolithically integrated optical elements is presented. A 275-nm period detuned second-order diffraction grating on the p-doped side layer is combined with a refractive lens transferred into the GaAs substrate so that outcoupling and beam-shaping functions are decoupled. The high-power device produces a circular spot and demonstrates the potential of dual optics integration in broad-area semiconductor diodes.

Journal Article↗
PubMed2004

Definition and variation of human endogenous retrovirus H.

We defined the abundant human endogenous retrovirus group HERV-H based on pol similarity. Among 3661 pol-containing elements, 1124 integrations were similar to HERV-H RGH2 pol using translated pol sequences. A clustering procedure lessened these to 234 representatives, amenable to detailed study. Among the 1124, 926 clustered into HERV-H and 106 into adjacent HERV-H-like, the remainder being more distant to HERV-H. The HERV-H group was divided into RTVLH2-like (705 elements) and RGH2-like (77 elements) subgroups. Among 926 HERV-H, LTR differences were 1-33%, 10% had env, 78% had gag, 66% had a histidine primer binding site (PBS), and 3% (both subgroups) had a phenylalanine PBS. Allelic differences in env were studied using a convenient temperature gradient gel electrophoresis (TGGE) method and a genomic single nucleotide polymorphism (SNP) search. A pattern of abundant defective elements and less abundant less defective ones led us to formulate a "midwife" master model where more complete elements help the others in trans to transpose.

Amino Acid Sequence↗
PubMed1991

Introduction of the transposable element mariner into the germline of Drosophila melanogaster.

A chimeric white gene (wpch) and other constructs containing the transposable element mariner from Drosophila mauritiana were introduced into the germline of Drosophila melanogaster using transformation mediated by the P element. In the absence of other mariner elements, the wpch allele is genetically stable in both germ cells and somatic cells, indicating that the peach element (i.e., the particular copy of mariner inserted in the wpch allele) is inactive. However, in the presence of the active element Mos1, the wpch allele reverts, owing to excision of the peach element, yielding eye-color mosaics and a high rate of germline reversion. In strains containing Mos1 virtually every fly is an eye-color mosaic, and the rate of wpch germline reversion ranges from 10 to 25%, depending on temperature. The overall rates of mariner excision and transposition are approximately sixfold greater than the rates in comparable strains of Drosophila simulans. The activity of the Mos1 element is markedly affected by position effects at the site of Mos1 insertion. In low level mosiac lines, dosage effects of Mos1 are apparent in the heavier level of eye-color mosaicism in Mos1 homozygotes than in heterozygotes. However, saturation occurs in high level mosaic lines, and then dosage effects are not observed. A pBluescribe M13+ plasmid containing Mos1 was injected into the pole plasm of D. melanogaster embryos, and the Mos1 element spontaneously integrated into the germline at high efficiency. These transformed strains of D. melanogaster presently contain numerous copies of mariner and may be useful in transposon tagging and other applications.

Alleles↗
PubMed2000

Ligand-triggered stabilization of vitamin D receptor/retinoid X receptor heterodimer conformations on DR4-type response elements.

Nuclear receptors integrate an incoming signal in the form of a nuclear hormone by undergoing a conformational change that results via co-activator proteins in an activation of the basal transcriptional machinery. The vitamin D(3) receptor is the nuclear receptor for 1alpha,25-dihydroxyvitamin D(3 )(1alpha,25(OH)(2)D(3)) and is known to function as a heterodimer with the retinoid X receptor on DR3-type 1alpha,25(OH)(2)D(3) response elements. Here, it could be demonstrated that DR4-type response elements are at least as effective as DR3-type 1alpha,25(OH)(2)D(3) response elements. Gel shift clipping analysis showed that vitamin D(3) receptor-retinoid X receptor heterodimers form in response to 1alpha, 25(OH)(2)D(3) and retinoid X receptor ligands, the pan-agonist 9-cis retinoic acid (9cRA) and the retinoid X receptor-selective retinoid CD2425, different conformations on the DR4-type element of the rat Pit-1 gene. Interestingly, on this response element the heterodimeric complexes of retinoid X receptor with the thyroid hormone receptor, the retinoic acid receptor and the benzoate ester receptor also displayed characteristic individual ligand-dependent complex formation. On the level of complex formation, utilizing DNA affinity and functional assays, only vitamin D(3) receptor-retinoid X receptor heterodimers showed a synergistic interaction of both ligands. However, the sensitivity of vitamin D(3) receptor-retinoid X receptor heterodimers to 1alpha,25(OH)(2)D(3) was found to be much higher than to retinoid X receptor ligands. Taken together, this study demonstrates a unique interaction potential of vitamin D(3) receptor and retinoid X receptor but also establishes DR4-type response elements as multi-functional DNA binding sites with a potential to integrate various hormone signalling pathways.

Animals↗
PubMed2005

[Modeling vocal-fold vibration via integrating two-mass model with finite-element method].

Modeling vocal-fold vibration is extremely significant in realizing the vibration properties of human vocal folds and investigating their physiological and pathological characteristics. A combined model presented is two mass-finite element (T-F) model, which integrates all merits of both the finite element method (FEM) model and the asymmetric two-mass model of vocal folds. The high-speed glottis graph (HGG) can also be synthesized by the model. The result shows that T-F model can simulate the vibration behavior of normal and pathological vocal folds in a more realistic way with competitively computational speed. Therefore, the T-F model is helpful to gaining a thorough understanding of the vibration properties of vocal folds.

Computer Simulation↗
PubMed2001

Institutionalization of a palliative and end-of-life care educational program in a medical school curriculum.

Stimulated by support from an R25 grant from the National Cancer Institute, we assembled a multidisciplinary team to design, implement, evaluate, and institutionalize in our medical school curriculum a training program to enable all students to graduate with basic competency in palliative and end-of-life care. In the fall of 1994, we reviewed the medical curriculum extensively to determine the need and optimal sites for integration of new educational modules. The freshman and junior years were found most suitable for our purposes; hence, behavioral objectives targeted at the freshman and junior medical student as learner were designed for the domain of palliative and end-of-life care. By 1996, negotiations with the medical school curriculum committee and with individual course masters secured permission and time allotments to include new coursework as required elements. We integrated approximately 20 hours of required training into the medical school curriculum, accomplished by modules that utilized small group learning, didactic presentations, out-of-classroom assignments, and practicum/experiential teaching methods. Freshman year curriculum consisted of a 3-hour module that considers the role of the physician in end-of-life care. Junior year training included a 1-hour module on advance directives and a 16-hour classroom and practicum course on hospice and end-of-life care. Performance-based assessment revealed that the students achieved the behavioral objectives. Furthermore, the students perceived benefit from the training and concluded that palliative care education should be a required part of their medical school experience. In September 2000, the medical school's Clinical Years Committee officially designated the palliative and end-of-life care training modules a mandatory part of the curriculum, with satisfactory completion a requirement for graduation.

Attitude to Death↗
PubMed2005

Spatiotemporal characteristics of form analysis in the human visual cortex revealed by rapid event-related fMRI adaptation.

The integration of local elements to coherent forms is at the core of understanding visual perception. Accumulating evidence suggests that both early retinotopic and higher occipitotemporal areas contribute to the integration of local elements to global forms. However, the spatiotemporal characteristics of form analysis in the human visual cortex remain largely unknown. The aim of this study was to investigate form analysis at different spatial (global vs. local structure) and temporal (different stimulus presentation rates) scales across stages of visual analysis (from V1 to the lateral occipital complex-LOC) in the human brain. We used closed contours rendered by Gabor elements and manipulated either the global contour structure or the orientation of the local Gabor elements. Our rapid event-related fMRI adaptation studies suggest that contour integration and form processing in early visual areas is transient and limited within the local neighborhood of their cells' receptive field. In contrast, higher visual areas appear to process the perceived global form in a more sustained manner. Finally, we demonstrate that these spatiotemporal properties of form processing in the visual cortex are modulated by attention. Attention to the global form maintains sustained processing in occipitotemporal areas, whereas attention to local elements enhances their integration in early visual areas. These findings provide novel neuroimaging evidence for form analysis at different spatiotemporal scales across human visual areas and validate the use of rapid event-related fMRI adaptation for investigating processing across stages of visual analysis in the human brain.

Adaptation, Psychological↗
PubMed1993

[Integration of a nursing model into a local community service center].

Four years ago, maternal/child health nurses from the Metro CLSC in Montreal found themselves in a crisis situation. They were unable to evaluate their work--which consisted of varying tasks and the need for these nurses to be everywhere at the same time. A need to reflect on the situation prompted the team to meet for three hours twice monthly to analyze the problems and establish a plan of action. A nurse-counsellor guided the initial process. A post-natal home visit was chosen as an example for discussion. The group conceded that each member of the perinatal team had a different philosophy and nursing approach. The team consisted of nurses of various ages, experiences and educational backgrounds. Some nurses felt more comfortable expressing themselves in English while others preferred French. At times this group diversity hindered the communication of ideas as well as the ability to reach a consensus about required practice changes. The McGill Nursing model from McGill University was chosen and integrated into the team's practice. The author presents this model and outlines it's advantages and disadvantages. She illustrates this model with the use of an ecomap designed by Wright and Leahy (1984). This nursing model addresses the use of forces within each individual as well as the family. Since it takes into account the extended family, it allows a global approach to care. The article focuses on the essential elements of integrating the model, including it's development and how it was accepted by these nurses. According to the author, the process of changing to this model is dynamic and continuous.(ABSTRACT TRUNCATED AT 250 WORDS)

Community Health Nursing↗
PubMed1985

Structure and unusual characteristics of a new family of transposable elements in the sea urchin Strongylocentrotus purpuratus.

The transposable element family TU of the sea urchin Strongylocentrotus purpuratus, a higher eucaryote, has recently been described (D. Liebermann, B. Hoffman-Liebermann, J. Weinthal, G. Childs, R. Maxson, A. Mauron, S.N. Cohen, and L. Kedes, Nature [London] 306:342-347, 1983). A member of this family, TU4, has an insertion, called ISTU4, of non-TU DNA. ISTU4 is a member of a family of repetitive sequences, which are present in some 1,000 copies per haploid S. purpuratus genome (B. Hoffman-Liebermann, D. Liebermann, L.H. Kedes, and S.N. Cohen, Mol. Cell. Biol. 5:991-1001, 1985). We analyzed this insertion to determine whether it is itself a transposable element. The nucleotide sequence of ISTU4 was determined and showed an unusual structure. There are four, approximately 150 nucleotides long, imperfect direct repeats followed by a single truncated version of these repeats. This region is bounded at either side by approximately 100-nucleotide-long sequences that are not related to each other or to the repeats. Nucleotide sequences at the boundaries of ISTU4-homologous and flanking regions in five genomic clones show that ISTU4 represents a family of sequences with discrete ends, which we call Tsp elements. We showed that the genomic locus that carries a Tsp element in one individual was empty in other individuals and conclude that Tsp elements are a new and different type of transposable element. Tsp elements lack two features common to most other transposable elements: Tsp integration does not result in the duplication of host DNA, and there are no inverted repeats at their termini, although short inverted repeats are present at a distance from the termini.

Animals↗
PubMed2000

[Transposition and inheritance of Bordetella Tn-element in Escherichia coli K12].

B. pertussis genetically mobile element TnBp3 integrates the plasmid in E. coli chromosome. During culturing under nonselective conditions the majority of cells of some E. coli strains lose the kanamycin resistance marker, which indicates the instability of TnBp3 inheriting. The stability of inheriting the integrated structure is higher in E. coli cells with recB-21 recC-12 sbcB-2 mutations. The role of RecBC recombination system in extrusion of TnBp3 is discussed.

Anti-Bacterial Agents↗
PubMed1993

Coronary atherosclerosis and chemical trace elements in the hair. A canonical correlation study of autopsy subjects, using an atherometric system and the X-ray fluorescence analysis.

An atherometric system (AS) was used to study coronary atherosclerotic lesions of a sample of 73 autopsy subjects. The content of nine chemical elements in the hair (K, Ca, Zn, Br, Sr, Pb, S, Cl, Cu) and the rates Zn/Cu and Ca/K were determined by energy dispersive X-ray fluorescence (EDXRF) analysis. Some canonical correlation analyses (CCA) were made of different combinations of chemical elements contents and of the following descriptive arterial variables of As: fatty streaks, fibrous plaques, severe (complicated plus calcified), plaques, and total atherosclerosis and the three weighted indices of AS, i.e. obstruction, stenosis and benignity. The arterial variables were obtained from the three major epicardial branches of the coronary arteries. Similar CCA analyses were performed to correlate chemical elements of the hair with some heart variables of AS, such as heart weight and estimated total volume of myocardium damaged by fibrosis and/or necrosis. The most remarkable results were as follows: Combinations of Pb, Ca/K, Zn/Cu and Fe, Ca/K, Zn/Cu were always strongly correlated with fatty streaks, fibrous plaques and severe plaques of the three coronary artery branches and the total coronary artery system, with the only exception of the left circumflex coronary artery when Fe was included. Similar results were recorded from obstruction, stenosis and benignity indices of AS. These two combinations of chemical elements were also correlated with the heart variables of AS. When the group of elements was integrated by Br, Ca/K, Zn/Cu, there were significant results with the heart variables, but not with the arterial variables of the AS.

Autopsy↗
PubMed1998

School-based health centers and school nurses: cementing the collaboration.

As school health personnel respond to the changing needs of children, new models are being developed and traditional models are being reexamined. The role of the school nurse is expanding at the same time as school-based health centers are increasing in number. Partnerships between school-based health centers and school nurses are critical for the success of school-based health centers, and partnerships will enhance and expand roles for school nurses. This paper clarifies the role of each in three areas: collaboration, communication, and cooperation. In addition, obstacles to partnerships are examined. The goal of this collaboration is a shared vision for the continuum of school health services in which school nurse and school health center serve integral roles. Elements for successful collaboration between nurse and health center are reviewed, including clarifying roles, shared leadership and program ownership, cooperative training and continuing education, negotiating conflict, and most importantly, maintaining mutual support and respect.

Communication↗
PubMed1994

Human immunodeficiency virus type 1 may preferentially integrate into chromatin occupied by L1Hs repetitive elements.

Human DNA flanking sites of eight human immunodeficiency virus type 1 (HIV-1) proviral integrations have been analyzed in isolates derived both from integrations in an infected individual and from tissue culture. Sequence analysis encompassing 80-3000 bp of human DNA on one or both sides of the site of integration revealed that seven of the eight HIV-1 proviruses had integrated directly into or within one nucleosome's distance from an L1Hs or Alu repetitive element. To compare this with the frequency at which human L1 or Alu elements sharing > or = 70% identity with L1Hs and Alu consensus sequences would be encountered at random, > 200 bp from each of 82 individual anonymously cloned segments of human DNA were sequenced: L1Hs elements were encountered in 8.5% of the 82 clones and Alu elements were encountered in 13.4+ by using these homology windows. From these data it appears that HIV-1 integrates into or near L1Hs elements with an approximately 6-fold higher frequency than would be expected if HIV-1 integration events were distributed uniformly throughout the genome. A cumulative binomial probability test shows that there is a 0.26% chance that one would arrive at these figures by chance and puts the data well within a 99% confidence interval. We propose that sites of L1Hs and Alu insertions originally occurred in regions of chromatin that were more easily accessible to the retroposon machinery and that these regions are now acting as preferred integration sites for HIV-1.

Base Sequence↗
PubMed2026

Genome-wide identification and cold-stress-responsive expression analysis of the NOX gene family in Cucumis melo.

NADPH oxidases (NOXs) are crucial enzymes for reactive oxygen species (ROS) generation in plants and play vital roles in growth, development, and stress responses. To elucidate the sequence characteristics of the NOX gene family and its low-temperature response patterns in melon (Cucumis melo L.), this study conducted genome-wide identification and expression profiling of NOX family members using bioinformatics analysis, RNA-seq transcriptome sequencing, and real-time quantitative PCR (RT-qPCR). The results revealed that eight NOX members were identified in the melon genome, distributed across six chromosomes. All members harbored conserved domains including Ferric_reductase, FAD_binding_8, NAD_binding_6, and NADPH_Ox, and the encoded proteins were generally basic and hydrophilic. Phylogenetic analysis classified the NOX proteins into five subgroups. Synteny analysis indicated the presence of only one pair of intraspecific duplicated genes in melon, which was under purifying selection. The promoter regions contained multiple hormone- and stress-responsive cis-acting elements, with CmNOX2 and CmNOX4 harboring low-temperature responsive elements. Following treatment at 4℃ for 24 h and 48 h, leaf relative electrolyte leakage (REL) increased from 28.33% to 42.67% and 52.67%, respectively; transcriptome analysis identified 5,633 and 6,882 differentially expressed genes (DEGs), respectively. Cold-responsive genes exhibited significant differential expression, with SLAC1 and CPK19 showing sustained upregulation. RT-qPCR results demonstrated that the expression of CmNOX2, CmNOX5, CmNOX6, and CmNOX7 was significantly downregulated after low-temperature treatment, whereas CmNOX4 expression was significantly upregulated at 48 h. Integrating promoter elements and expression characteristics, CmNOX4 may represent an important candidate gene involved in melon low-temperature response. This study systematically characterized the structure, evolution, and expression patterns of the melon NOX gene family, identified candidate genes responsive to low temperature, and provides a reference for further investigation into the mechanisms underlying melon cold adaptation.

Cucumis melo↗
PubMed2026

Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes.

Toxin-antitoxin systems (TAs) are widespread in bacterial genomes. Yet, their integration, persistence, and impact in chromosome dynamics remain unclear. Here, we identified 80 type II TAs in the single chromosome of Photorhabdus laumondii TT01, 50 of which were experimentally validated. Comparative analysis across the Photorhabdus genus revealed a highly heterogeneous distribution, with TAs frequently clustering within discrete genomic regions, either alone or associated with cointegrate-forming transposases and integrases. TAs rarely clustered with other putative defense systems and are preferentially associated with different types of recombinases, suggesting distinct pathways of acquisition for the two types of functions. Functional analyses showed that most validated TAs display addictive properties and stabilize plasmids. These addictive TAs are preferentially located in genomic regions characterized by high gene turnover, consistent with recent acquisition events. Despite their plasmid-stabilizing capacity, TAs do not promote long-term conservation of their immediate chromosomal neighborhoods. Instead, we observed frequent TA loss, either through complete deletion or toxin pseudogenization, indicating relaxed selection for their persistence in bacterial lineages. We propose a stepwise model for TA evolution in bacterial chromosomes: initial acquisition mediated by mobile genetic elements, preferential integration into permissive genomic regions, subsequent genetic streamlining of linked loci, and progressive gene loss. The short-lasting linkage between TAs and their genomic neighborhoods is consistent with the view that TA modules can behave as autonomous, selfish genetic elements.

Journal Article↗
PubMed2003

The Karyote physico-chemical genomic, proteomic, metabolic cell modeling system.

Modeling approaches to the dynamics of a living cell are presented that are strongly based on its underlying physical and chemical processes and its hierarchical spatio-temporal organization. Through the inclusion of a broad spectrum of processes and a rigorous analysis of the multiple scale nature of cellular dynamics, we are attempting to advance cell modeling and its applications. The presentation focuses on our cell modeling system, which integrates data archiving and quantitative physico-chemical modeling and information theory to provide a seamless approach to the modeling/data analysis endeavor. Thereby the rapidly growing mess of genomic, proteomic, metabolic, and cell physiological data can be automatically used to develop and calibrate a predictive cell model. The discussion focuses on the Karyote cell modeling system and an introduction to the CellX and VirusX models. The Karyote software system integrates three elements: (1) a model-building and data archiving module that allows one to define a cell type to be modeled through its reaction network, structure, and transport processes as well as to choose the surrounding medium and other parameters of the phenomenon to be modeled; (2) a genomic, proteomic, metabolic cell simulator that solves the equations of metabolic reaction, transcription/translation polymerization and the exchange of molecules between parts of the cell and with the surrounding medium; and (3) an information theory module (ITM) that automates model calibration and development, and integrates a variety of data types with the cell dynamic computations. In Karyote, reactions may be fast (equilibrated) or slow (finite rate), and the special effects of enzymes and other minority species yielding steady-state cycles of arbitrary complexities are accounted for. These features of the dynamics are handled via rigorous multiple scale analysis. A user interface allows for an automated generation and solution of the equations of multiple timescale, compartmented dynamics. Karyote is based on a fixed intracellular structure. However, cell response to changes in the host medium, damage, development or transformation to abnormality can involve dramatic changes in intracellular structure. As this changes the nature of the cellular dynamics, a new model, CellX, is being developed based on the spatial distribution of concentration and other variables. This allows CellX to capture the self-organizing character of cellular behavior. The self-assembly of organelles, viruses, and other subcellular bodies is being addressed in a second new model, VirusX, that integrates molecular mechanics and continuum theory. VirusX is designed to study the influence of a host medium on viral self-assembly, structural stability, infection of a single cell, and transmission of disease.

Animals↗
PubMed1993

Trans-activation and stable integration of the maize transposable element Ds cotransfected with the Ac transposase gene in transgenic rice plants.

To develop an efficient gene tagging system in rice, a plasmid was constructed carrying a non-autonomous maize Ds element in the untranslated leader sequence of a hygromycin B resistance gene fused with the 35S promoter of cauliflower mosaic virus. This plasmid was cotransfected by electroporation into rice protoplasts together with a plasmid containing the maize Ac transposase gene transcribed from the 35S promoter. Five lines of evidence obtained from the analyses of hygromycin B-resistant calli, regenerated plants and their progeny showed that the introduced Ds was trans-activated by the Ac transposase gene in rice. (1) Cotransfection of the two plasmids is necessary for generation of hygromycin B resistant transformants. (2) Ds excision sites are detected by Southern blot hybridization. (3) Characteristic sequence alterations are found at Ds excision sites. (4) Newly integrated Ds is detected in the rice genome. (5) Generation of 8 bp target duplications is observed at the Ds integration sites on the rice chromosomes. Our results also show that Ds can be trans-activated by the transiently expressed Ac transposase at early stages of protoplast culture and integrated stably into the rice genome, while the cotransfected Ac transposase gene is not integrated. Segregation data from such a transgenic rice plant carrying no Ac transposase gene showed that four Ds copies were stably integrated into three different chromosomes, one of which also contained the functional hph gene restored by Ds excision. The results indicate that a dispersed distribution of Ds throughout genomes not bearing the active Ac transposase gene can be achieved by simultaneous transfection with Ds and the Ac transposase gene.

Base Sequence↗