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PubMed1985

Chromosomal rearrangements associated with LINE elements in the mouse genome.

Two segments of DNA that have apparently inserted in the interval between the two adult beta-globin genes in BALB/c (Hbbd haplotype) but not in C57B1/10 (Hbbs haplotype) mouse strains have been described (1). These putative insertions, each about 1000 bp in length, mapped near a repetitive element. To determine the precise position of these alleged insertions, their target sites, and the nature of their boundaries, we cloned and sequenced the appropriate regions of both chromosomes. One of the two segments is not an insertion but rather a region between two independently integrated L1 repetitive elements (LINEs) (2), one in Hbbd and the other in the Hbbs chromosome. The other segment is an insertion of 940 bp which is located within the L1 element in the Hbbd chromosome. This insert is unusual in that it exists in only one copy in the BALB/c genome.

Animals↗
PubMed1989

[Organization of the bony nasal septum and its homologues I. Os alare et systema integratum fronto-alare in birds].

The aim of the investigation was the systematization of the bony elements in the orbito-nasal septum and the verification of the notion "mesoethmoideum" in birds. The macerated skulls of adult ostrichs, chickens and pheasants were examined by use of the optic- and radiophotography. In ostrichs were the characteristic interorbital septum as the alar bone integrated with the elements of the prefrontal bones. In chickens were two biochemical systems: a) the anterior alar lamina and b) posterior part without bony trabecular diploe elements. In all birds the author did not found any "mesosthmoideum". These presented facts led to further study in birds, fishes, mammals and man.

Animals↗
PubMedDate not supplied

Doe's quality system program: cooperative development and implementation.

Implementation of a Quality Systems approach to making defensible environmental program decisions depends upon multiple, interrelated components. Often, these components are developed independently and implemented at various facility and program levels in an attempt to achieve consistency and cost savings. The U.S. Department of Energy, Office of Environmental Management (DOE-EM) focuses on three primary system components to achieve effective environmental data collection and use. (1) Quality System guidance, which establishes the management framework to plan, implement, and assess work performed; (2) A Standardized Statement of Work for analytical services, which defines data generation and reporting requirements consistent with user needs; and (3) A laboratory assessment program to evaluate adherence of work performed to defined needs, e.g., documentation and confidence. This paper describes how DOE-EM fulfills these requirements and realizes cost-savings through participation in interagency working groups and integration of system elements as they evolve.

Cost-Benefit Analysis↗
PubMed2004

Diversity in the lysis-integration region of oenophage genomes and evidence for multiple tRNA loci, as targets for prophage integration in Oenococcus oeni.

The central genomic regions of Oenococcus oeni phages fOg30 and fOgPSU1 have been compared with the equivalent regions of oenophages fOg44 and phi 10MC. In all cases, an almost identical endolysin gene was followed by one of two orfs, encoding putative holins (orf117 and orf163). The fOg44 endolysin was established as a secretory protein when expressed in Lactococcus lactis. Orf117 (from fOg44) promoted lysis of Escherichia coli cultures upon induction of a defective lambda Sam7 prophage, but Orf163 (from fOg30) failed to elicit a lysis response in this system. fOg44 and fOgPSU1 were shown to integrate at the 3' end of a tRNA(Glu) and a tRNA(Lys), respectively. Searching the available sequence of the O. oeni MCW genome for attP-like elements, two other tRNA targets could be proposed for prophage establishment. Between the lysis and integration elements, a diverse cluster of genes (absent in phi 10MC) was observed. One common gene in this "lysogenic conversion cluster" was experimentally confirmed as a transcriptional repressor, affecting the expression of a putative permease gene.

Amino Acid Sequence↗
PubMed1997

Identification of a chromosomal Shigella flexneri multi-antibiotic resistance locus which shares sequence and organizational similarity with the resistance region of the plasmid NR1.

The ampicillin resistance gene from Shigella flexneri 2a strain YSH6000 was cloned and shown by Southern hybridization analysis to be closely linked to the previously cloned streptomycin, chloramphenicol, and tetracycline resistance determinants, which are borne on a chromosomally integrated 99-kb element. Analysis of this chromosomal multi-antibiotic resistance locus revealed that it had a high level of sequence and organizational similarity to an equivalent region of the Shigella R-plasmid, NR1. However, the chromosomal locus exhibited several differences, including the presence of two stretches of sequence derived from IS elements, the precise insertion of a beta-lactamase encoding oxal cassette into the Tn21-borne integron In2, a possible 17.5-kb deletion, and the loss or inactivation of the mercury resistance determinant. Based on these data, it is proposed that the chromosomal locus arose following integration of an NR1-like plasmid.

Ampicillin↗
PubMedDate not supplied

The National Alzheimer's Coordinating Center (NACC) Database: an Alzheimer disease database.

The National Alzheimer's Coordinating Center (NACC) is responsible for developing and maintaining a database of patient information collected from the 29 Alzheimer disease centers (ADCs) funded by the National Institute on Aging. Each of the centers collects center-determined data elements on patients enrolled into its center and transmits a minimum dataset to NACC. Data are managed differently at each center depending on that center's research needs. The centers' data systems vary from a single personal computer running spreadsheet software to a network of servers running an advanced data management system such as Oracle. The challenge for NACC is to expand and adjust previously collected data elements into an integrated database that could be used for administrative as well as research purposes. In addition, NACC sought to allow the centers to have the flexibility they needed for data submission. To accomplish this task, NACC designed a database that contained separate specific datasets each with individual data elements. NACC also designed a data management system to easily collect and manage these data. The NACC web site (www.alz.washington.edu) was created to allow access to the data.

Alzheimer Disease↗
PubMed1997

A highly efficient and stable system for site-specific integration of genes and plasmids into the phage phiLC3 attachment site (attB) of the Lactococcus lactis chromosome.

An integration vector system based on the site-specific integration apparatus of the temperate lactococcal bacteriophage phiLC3 was developed. A 1.6-kb recombinogenic DNA cassette, containing the phiLC3 integrase gene (int) and the phage attachment site (attP), mediated site-specific integration of a single marker-gene, as well as of a replication-thermosensitive (-ts) plasmid (pINT2), into the phiLC3 attB site of Lactococcus lactis subsp. lactis LM0230 chromosome after introduction of the DNA into the cells by electroporation. Both the marker gene and the pINT2 plasmid were stably inserted as single copies in an orientation-specific and integrase-dependent manner, the pINT2-ts replicon being stably maintained at temperatures both permissive and non-permissive for plasmid-directed replication. Essentially all transformants obtained with the pINT2 plasmid appeared to be integrants, demonstrating the remarkably high efficiency of the system. This high efficiency rendered possible the detection of transformation-plus-integration events using DNA directly obtained from ligase reaction mixtures, thus avoiding initial subcloning in a non-lactococcal strain and subsequent cointegration of foreign replication functions into the chromosome of L. lactis. The above results, the observation that the phiLC3 attB site appear to be conserved in L. lactis, and the fact that the int-attP cassette functions efficiently in a non-phiLC3-host strain, show that the phiLC3 site-specific integration apparatus provides an efficient and 'food grade' tool for stable integration of genetic elements into the chromosome of L. lactis.

Bacteriophages↗
PubMed2003

Feasibility of calculating morphology-dependent resonance peaks by numerical methods.

We investigate the feasibility of numerically calculating morphology-dependent resonance (MDR) peaks. To do so, one has to calculate the scattering intensities numerically and determine how difficult it is to numerically predict the position and the magnitude of the MDR peaks. However, at present, in practice it is impossible to calculate MDR peaks with a personal computer because so much computing time is required. Therefore the surface values of the Debye potential and its derivative for a homogeneous sphere are obtained from Mie's analytical solution and then used in integral equations to give the scattering intensities at a specific position of infinity by numerical integrations. It is shown that if a sufficient number of surface elements are used, the MDR peaks are exactly calculated for a homogeneous sphere with refractive index of 1.5, 1.4, and 1.3 up to a size parameter of 20. One can conjecture the number of finite and boundary elements necessary to numerically compute accurate scattering intensities. It should be also noted that the number of surface elements necessary for exact integration shows peaks similar to MDR peaks with respect to the size parameter. Therefore one will need many more elements at the size parameter at which the MDR occurs.

Journal Article↗
PubMed2005

Design of monolimb using finite element modelling and statistics-based Taguchi method.

BACKGROUND: Monolimb is a transtibial prosthesis having the socket and shank molded into one piece of thermoplastic material. If properly designed, the shank of a monolimb can have a controlled deflection during walking which simulates the ankle joint motions to some extent. However, there is no clear guidance for the design of monolimb considering the dilemma between shank flexibility and structural integrity. METHODS: Finite element analysis was used to simulate structural tests based on ISO10328 on monolimbs of different configurations. Statistics-based Taguchi method was employed to identify the significance of each design factor in controlling the deformation and stress within monolimbs. The design factors considered were the thickness of the thermoplastics, anteroposterior and medialateral dimensions of the elliptical shank, and depth of the posterior seam line. By progressively fine-tuning the design factors, the monolimb configuration was optimized giving offering appropriate flexibilities of the shank and would not structurally fail in normal uses. Experimental structural test was used to validate the finite element model. FINDINGS: Anteroposterior dimension of the shank was shown to be the most important design factor determining the peak von Mises stress values, deformation and dorsiflexion angles of monolimbs. Depth of seam line appears much less important than the other three factors. A monolimb fulfilling the design requirements was suggested. Experimental test results reasonably matched with the finite element results. INTERPRETATION: Finite element analysis and Taguchi method was shown to be an effective method in optimizing the structural design of prostheses. Further prosthetic design can be facilitated based on the degree of importance of the design factors on the structural behavior of the prosthesis. Gait analysis of amputees using the suggested monolimb design is needed in the future.

Algorithms↗
PubMed1985

Regulation of the expression of iso 2-cytochrome c gene in S. cerevisiae: cloning of the positive regulatory gene CYP1 and identification of the region of its target sequence on the structural gene CYP3.

CYP1 is a trans acting regulatory locus modulating both iso 1- and iso 2-cytochrome c synthesis. Genetical analysis of various mutated alleles has allowed us to identify the gene product as a positive regulatory element. The region of the target sequence of the CYP1 product on the iso 2-cytochrome c structural gene was located by molecular and genetic analysis of two cis acting mutations located at the CYP3 locus: CYP3-36 and CYP3-4, which have been shown to arise from the integration of TY1 elements near the promoter site. Determination of the amount of iso 2-cytochrome c synthesized by strains bearing various genetic constructions, in which the cis acting mutations were associated with different alleles of the CYP1 trans acting locus, showed that TY1 inserted into CYP3-36 extinguishes the activation function due to a mutated overproducer allele CYP1-18, while CYP3-4 amplifies this function. This result identifies at least a part of the target sequence of the CYP1 product within the region separating the two TY1 insertions. To clone the CYP1 gene, we took advantage of the iso 2-cytochrome c overproducer phenotype of the mutated allele CYP1-18, which confers a Lactate+ phenotype on an iso 1-cytochrome c-deficient strain. Such a phenotype allowed the isolation of a recombinant plasmid YEpJFM1 carrying the mutated allele, able to complement on lactate medium a lactate- recipient strain. The identity of the YEpJFM1 sequence with the chromosomal gene was confirmed by homologous recombination at the CYP1 locus.

Alleles↗
PubMed1993

The lytic origin of herpesvirus papio is highly homologous to Epstein-Barr virus ori-Lyt: evolutionary conservation of transcriptional activation and replication signals.

Herpesvirus papio (HVP) is a B-lymphotropic baboon virus with an estimated 40% homology to Epstein-Barr virus (EBV). We have cloned and sequenced ori-Lyt of herpesvirus papio and found a striking degree of nucleotide homology (89%) with ori-Lyt of EBV. Transcriptional elements form an integral part of EBV ori-Lyt. The promoter and enhancer domains of EBV ori-Lyt are conserved in herpesvirus papio. The EBV ori-Lyt promoter contains four binding sites for the EBV lytic cycle transactivator Zta, and the enhancer includes one Zta and two Rta response elements. All five of the Zta response elements and one of the Rta motifs are conserved in HVP ori-Lyt, and the HVP DS-L leftward promoter and the enhancer were activated in transient transfection assays by the EBV Zta and Rta transactivators. The EBV ori-Lyt enhancer contains a palindromic sequence, GGTCAGCTGACC, centered on a PvuII restriction site. This sequence, with a single base change, is also present in the HVP ori-Lyt enhancer. DNase I footprinting demonstrated that the PvuII sequence was bound by a protein present in a Raji nuclear extract. Mobility shift and competition assays using oligonucleotide probes identified this sequence as a binding site for the cellular transcription factor MLTF. Mutagenesis of the binding site indicated that MLTF contributes significantly to the constitutive activity of the ori-Lyt enhancer. The high degree of conservation of cis-acting signal sequences in HVP ori-Lyt was further emphasized by the finding that an HVP ori-Lyt-containing plasmid was replicated in Vero cells by a set of cotransfected EBV replication genes. The central domain of EBV ori-Lyt contains two related AT-rich palindromes, one of which is partially duplicated in the HVP sequence. The AT-rich palindromes are functionally important cis-acting motifs. Deletion of these palindromes severely diminished replication of an ori-Lyt target plasmid.

Animals↗
PubMed2002

Inactivation of the Fas gene by Alu insertion: retrotransposition in an intron causing splicing variation and autoimmune lymphoproliferative syndrome.

Mutations in the Fas (apo-1, CD95) gene result in autoimmune lymphoproliferative syndrome (ALPS). These mutations are dominated by small deletions and point mutations that result in splicing errors or missense changes. We report here a novel mutation caused by retrotransposon insertion, which results in loss of exon 8 and ALPS. A father and son suffering from recurrent lymphadenopathy were examined for resistance to Fas-mediated apoptosis. A functional defect was detected and RT-PCR analysis revealed two different copies of Fas mRNA, one normal and a second shorter version lacking exon 8. DNA analysis of the genomic region between exons seven and nine in the longer copy revealed two PCR products, one being 331 base pairs (bp) longer than expected. Sequencing revealed that intron 7 had undergone an insertion event with an Alu element (99.31% homology with Alu-Sb1) of 331 bp. This element included a 34-bp Poly A tract that was flanked on each side by a perfect 17 bp direct duplication of the target site. Both patients were heterozygous for the mutated allele that produced Fas mRNA lacking exon 8, although not due to loss of a splice junction. The structure of the insertion suggests that the Alu element may have integrated by retrotransposition, and represents the first report of a retrotransposon causing ALPS.

Alu Elements↗
PubMed2006

Programming strategies for rapid aiming movements under simple and choice reaction time conditions.

Increases in reaction time (RT) as a function of response complexity have been shown to differ between simple and choice RT tasks. Of interest in the present study was whether the influence of response complexity on RT depends on the extent to which movements are programmed in advance of movement initiation versus during execution (i.e., online). The task consisted of manual aiming movements to one or two targets (one- vs. two-element responses) under simple and choice RT conditions. The probe RT technique was employed to assess attention demands during RT and movement execution. Simple RT was greater for the two- than for the single-target responses but choice RT was not influenced by the number of elements. In both RT tasks, reaction times to the probe increased as a function of number of elements when the probe occurred during movement execution. The presence of the probe also caused an increase in aiming errors in the simple but not choice RT task. These findings indicated that online programming was occurring in both RT tasks. In the simple RT task, increased executive control mediated the integration between response elements through the utilization of visual feedback to facilitate the implementation of the second element.

Adolescent↗
PubMed2006

Viral determinants of integration site preferences of simian immunodeficiency virus-based vectors.

Preferential integration into transcriptionally active regions of genomes has been observed for retroviral vectors based on gamma-retroviruses and lentiviruses. However, differences in the integration site preferences were detected, which might be explained by differences in viral components of the preintegration complexes. Viral determinants of integration site preferences have not been defined. Therefore, integration sites of simian immunodeficiency virus (SIV)-based vectors produced in the absence of accessory genes or lacking promoter and enhancer elements were compared. Similar integration patterns for the different SIV vectors indicate that vif, vpr, vpx, nef, env, and promoter or enhancer elements are not required for preferential integration of SIV into transcriptionally active regions of genomes.

Cells, Cultured↗
PubMed2005

Intercurrent coccidiosis and necrotic enteritis of chickens: rational, integrated disease management by maintenance of gut integrity.

Coccidiosis and necrotic enteritis (NE) are globally common, sometimes intercurrent, diseases of poultry. The risk of NE, due to the Gram-positive bacterium Clostridium perfringens, has increased in recent years because of the voluntary or legally required withdrawal of the use of certain in-feed antibiotic growth promoters with anticlostridial activity. In-feed ionophorous anticoccidial drugs incidentally also possess anticlostridial activity. Such ionophores, although not banned, are usually precluded when live anticoccidial vaccines are used, potentially increasing yet further the risk of NE. This review provides information for the design of rational, integrated management strategies for the prevention and control of coccidiosis and NE in chickens by maintaining gut integrity. Because of differences in local availability of feed ingredients and national legislations regarding antibiotic growth promoters and anticoccidial vaccine licensing, no universal strategy is applicable. The diseases and their interactions are described under the headings of forms of disease, diagnosis, sources of infection, pathophysiological effects, predisposing factors, and control methods. Elements of gut integrity, which influences host predisposition and clinical responses to disease, include physical development, immune competence, gut enzyme activity, mucin production, gut flora and epithelial damage. Experimental studies of coccidiosis and NE are compared, and where possible reconciled, with field observations. Gaps in knowledge and necessary further experiments are identified. Insights are provided regarding interactions between coccidiosis, NE, and the use of live anticoccidial vaccines. Recent changes in NE prevalence in commercial flocks, and their possible causes, are discussed. The necessarily wide range of topics reviewed emphasizes the enormous complexity of this disease combination, and indicates the importance of a multidisciplinary approach in order to reduce its harmful impact on the world's poultry industry.

Animal Husbandry↗
PubMed1987

Site-specific integration and excision of pMEA100 in Nocardia mediterranei.

Nocardia mediterranei strain LBG A3136 contains the 23.7 kb element pMEA100 in a chromosomally integrated form as well as in the free state (Moretti et al. 1985). The integrated form of this element can be excised precisely from the Nocardia chromosome without any accompanying rearrangements in flanking chromosomal DNA. After transfer into plasmid-free mutant strains, pMEA100 reintegrates site specifically into its original chromosomal locus. The exact mapping of the pMEA100 integration site was accomplished by restriction analysis and DNA sequencing. The attachment site of pMEA100, the junctions of its integrated form and plasmid-free chromosomal DNA of N. mediterranei contain an identical 47 bp long sequence which is probably required for site-specific recombination connected with integration and excision of pMEA100. Only one such sequence was found in the chromosome of pMEA100-free N. mediterranei derivatives as suggested by the single integration locus.

Base Sequence↗
PubMed2001

T3-activation of the rat growth hormone gene is inhibited by a zinc finger/homeodomain protein.

Since the transcription factor Zfhep is expressed in somatotropes and binds the rat growth hormone (rGH) gene T3-response element (TRE), we investigated whether Zfhep regulates the response of this gene to T3. In cotransfection experiments, Zfhep did not regulate the native rGH promoter in the absence of T3. However, Zfhep repressed T3-mediated activation significantly in either GH(3) or JEG-3 cells. Up to 70% repression was mediated through the rGH TRE in a heterologous promoter (thymidine kinase), but was not observed with the idealized DR4 or chicken lysozyme F2 TREs. Zfhep apparently does not repress T3-mediated activation simply by competition for binding to DNA since the C-terminal DNA-binding domain of Zfhep (which is sufficient for DNA-binding) is not sufficient for repression and since cotransfection of excess thyroid hormone receptor (TR) did not prevent repression by Zfhep. These data indicate that the rGH TRE is a composite element that can integrate Zfhep and T3 regulation.

Animals↗
PubMed2002

Brain activity related to integrative processes in visual object recognition: bottom-up integration and the modulatory influence of stored knowledge.

We report evidence from a PET activation study that the inferior occipital gyri (likely to include area V2) and the posterior parts of the fusiform and inferior temporal gyri are involved in the integration of visual elements into perceptual wholes (single objects). Of these areas, the fusiform and inferior temporal gyri were more activated by tasks with recognizable stimuli than by tasks with unrecognizable stimuli. We propose that the posterior parts of the fusiform and inferior temporal gyri, compared with the inferior occipital gyri, are involved in higher level integration, due to the involvement of re-entrant activation from stored structural knowledge. Evidence in favor of this interpretation comes from the additional finding that activation of the anterior part of the left fusiform gyrus and a more anterior part of the right inferior temporal gyrus, areas previously associated with access to stored structural knowledge, was found with recognizable stimuli, but not with unrecognizable stimuli. This latter finding also indicates: (i) that subjects may not refrain from (automatically) identifying objects even if they only have to attend to the objects' global shape, and (ii) that perceptual and memorial processes can be dissociated on both functional and anatomical grounds. No evidence was obtained for the involvement of the parietal lobes in the integration of single objects.

Adult↗