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PubMed1995

The isolation of Ant1, a transposable element from Aspergillus niger.

A transposable element has been isolated from the industrially important fungus Aspergillus niger (strain N402). The element was identified as an insertion sequence within the coding region of the nitrate reductase gene. It had inserted at a TA site and appeared to have duplicated the target site upon insertion. The isolated element was found to be 4798 bp in length and contained 37-bp inverted, imperfect, terminal repeats (ITRs). The sequence of the central region of the element revealed an open reading frame (designated ORF1) which showed similarity, at the amino acid level, to the transposase of the Tc1/mariner class of DNA transposons. Another sequence within the central region of the element showed similarity to the 3' coding and downstream untranslated region of the amyA gene of A. niger. Sequence homology and structural features indicate that this element, which has been named Ant1 (A. niger transposon 1), is related to the Tc1/mariner group of DNA transposons. Ant1 is apparently present as a single copy in strain N402 of A. niger.

Amino Acid Sequence↗
PubMed2003

[Treatment for central neurocytoma: a meta-analysis based on the data of 358 patients].

BACKGROUND: Central neurocytomas are described as uncommon benign CNS lesions. Uncertainty exists about the most appropriate treatment regimen. This retrospective analysis compares four therapies for local control and overall survival: complete resection alone (KR), complete resection plus radiotherapy (KR-RT), incomplete resection alone (IR), and incomplete resection plus radiotherapy (ITR-RT). MATERIAL AND METHODS: The cases published in the literature since 1982 were reviewed for age, gender, extent of resection, atypical neurocytoma, radiotherapy, local control, and overall survival (minimum follow-up 12 months). From direct contact with the authors additional data were obtained providing more detailed information about the patients and a longer follow-up. Statistical analysis was performed with the Kaplan-Meier analysis and the log-rank test. RESULTS: Complete data were obtained from 358 patients (KR 118, KR-RT 35, IR 91, IR-RT 114). Local control was significantly better after KR, KR-RT and IR-RT than after IR (Figure 1). No significant difference was found between KR, KR-RT and IR-RT. Median time to progression was 36 (KR), 39 (KR-RT), 21 (IR) and 32 (IR-RT) months. The comparison of the four groups for overall survival demonstrated that KR provided a significantly better overall survival than IR (Figure 2). Overall survival rates were 99.2% and 86.1%, respectively. CONCLUSIONS: Complete resection is much more effective for the treatment of central neurocytoma than incomplete resection. After complete resection the additional benefit of postoperative radiotherapy remains unclear. After incomplete resection postoperative radiotherapy significantly improved local control, but not overall survival.

Adolescent↗
PubMed2004

Quantitative ultrasound and dual-energy X-ray absorptiometry in the prediction of fragility fracture in men.

Fragility fractures in men represent a major health problem, and this prompts a necessity for reliable tools for the identification of men at risk of fracture. In order to assess the ability of dual-energy X-ray absorptiometry (DXA) and quantitative ultrasound (QUS) in the prediction of fracture risk in men and whether their combination might be useful in a clinical setting, we studied 401 men (age range 45-82 years, mean 60.3+/-12.5), of whom 133 had osteoporotic fractures and 268 did not. In all subjects we measured bone mineral density at the lumbar spine (BMD-LS) and at the femur, calculating thereafter the standard femoral subregions: neck (BMD-FN), total hip (BMD-T), trochanter (BMD-TR), intertrochanter (BMD-ITR), and Ward's triangle (BMD-W), by DXA. We also performed ultrasound parameters at the calcaneus: speed of sound (SOS), broadband ultrasound attenuation (BUA) and Stiffness, by Achilles plus, and at the phalanxes: amplitude dependent speed of sound (AD-SoS) and the parameters of the graphic trace: bone transmission time (BTT), fast wave amplitude (FWA), signal dynamic (SDy) and ultrasound bone profile index (UBPI), by Bone Profiler. All DXA and QUS parameters, apart from FWA, were significantly (P<0.001) lower in patients with a history of fracture. BMD at the proximal femur showed the best ability in discriminating men with or without fractures. QUS at the heel showed discriminatory ability significantly better than QUS at the fingers. By logistic regression analysis, adjusted for age and BMI, BMD-T showed the best association with fragility fracture [odds ratio (OR)=3.43, 95% confidence interval (CI)=2.47-4.77]. Among QUS parameters, the highest value of the OR was shown by stiffness (OR=3.18, CI=2.27-4.48). FWA and SDy were not associated with fragility fractures in men. If DXA and QUS were combined, the prediction of the OR of fragility fracture events in men increases; in fact Stiffness was able to increase the OR when added to BMD-LS (OR=5.44, CI=3.16-10.13) and BMD-T (OR=6.08, CI=2.63-14.27). SOS and BUA showed a similar pattern. AD-SoS improved the prediction of fracture only when combined with BMD-LS (OR=4.36, CI=1.99-9.57). If BMD-LS and BMD-FN or BMD-T were combined, the value of the OR increases (OR=4.59, CI=2.27-9.25 and OR=4.68, CI=2.24-9.76), respectively. Our study supports the effectiveness of QUS in the identification of osteoporotic fractures in men. QUS seems to play an independent and complementary role, with respect to DXA, in order to enhance the power for predicting osteoporotic fractures in men.

Absorptiometry, Photon↗
PubMed2000

Features of the mammal mar1 transposons in the human, sheep, cow, and mouse genomes and implications for their evolution.

Mariner-like elements (MLE) belong to the Tc1/ mariner superfamily of class II transposons. We have analyzed the mariner related to the cecropia subfamily, and called mammal mar1, in four mammalian genomes, Bos taurus (Bovidae), Homo sapiens (Primata), Mus musculus (Rodentia), and Ovis aries (Ovidae). Three kinds of MLE sequences were found in all these species: full-length 1.3-kbp elements, shorter elements 80 bp-1.2 kbp, and single inverted terminal repeats (ITRs). All the 1.3-kbp genomic copies sequenced had an open reading frame encoding a transposase interrupted by stop codons or frame shifts. Phylogenetic analysis of the full-length elements suggested at least two distinct populations of mammal mar1 elements in each species. This was confirmed by using a statistical method that allows defining populations. Finally, the evolutionary origin of the mammal mar1 elements and the paradoxes are discussed.

Animals↗
PubMed2002

Aberrant transposition of a Tc1-mariner element, impala, in the fungus Fusarium oxysporum.

We previously determined that the impalaD transposable element of Fusarium oxysporum was able to mobilize a non autonomous copy of impala ( niaD::imp::hph), inserted in the niaD gene encoding nitrate reductase. Generally, mobilization results in the recovery of Nia(+) revertants at low frequency. In the course of this study, we recovered a transformant that gave rise to Nia(+) revertants at a high rate. These revertants displayed atypical phenotypes and showed a niaD hybridization pattern different from that in more typical revertants. Molecular analysis of the structure of the transformant and atypical revertants indicated that (i) in the transformant, two copies of impala, one defective and one active, were inserted at the same genomic locus in a head-to-head orientation; and (ii) all the revertants analyzed presented the same chromosomal rearrangement, an inversion resulting in the replacement of the niaD promoter by a new sequence containing a cryptic promoter. We also frequently observed additional DNA rearrangements (deletion or inversion) in these revertants. The sequences at the rearrangement junctions indicated the occurrence of a transposition event that used the ITRs (Inverted Terminal Repeats) of separate transposons arranged in direct orientation. These features can be interpreted as the consequences of an aberrant transposition process. Such a process may account for the rearrangements observed in some genomic regions containing multiple transposon ends, and could serve as a mechanism for the generation of genetic diversity.

Base Sequence↗
PubMed2001

Mobility of the piggyBac transposon in embryos of the vectors of Dengue fever (Aedes albopictus) and La Crosse encephalitis (Ae. triseriatus).

The re-emergence of arboviral diseases such as Dengue Fever and La Crosse encephalitis is primarily due to the failure of insect vector control strategies. The development of a procedure capable of producing stable germ-line transformants in the insect vectors of these diseases would bridge the gap between gene expression systems being developed to curb vector transmission and the identification of important genes and regulatory sequences and their reintroduction back into the insect genome in the form of vector control strategies. The transposable element piggyBac is capable of transposition in a variety of insect species, and could serve as a versatile insect transformation vector. Using plasmid-based excision and transposition assays, we report that this short-ITR transposon undergoes precise, transposase-dependent excision and transposition in embryos of Aedes albopictus and Aedes triseriatus, the vectors of Dengue fever and LaCrosse encephalitis, respectively. These assays allow us easily and rapidly to confirm and assess the potential utility of piggyBac as a gene transfer tool in a given species. piggyBac is an exceptionally mobile and versatile genetic transformation vector, comparable to other transposons currently in use for the transformation of insects. The mobility of the piggyBac element seen in both Ae. albopictus and Ae. triseriatus is further evidence that it can be employed as a germ-line vector in important insect disease vectors.

Aedes↗
PubMed2000

The degenerate DNA transposon Pat and repeat-induced point mutation (RIP) in Podospora anserina.

A degenerate DNA transposon, Pat, was identified in the genomes of various wild-type strains of the filamentous fungus Podospora anserina. In these strains, the number (approximately 20-25 copies per genome) and location of Pat sequences appear to be conserved. Two copies of Pat, one complete and one partial, were cloned and characterized. The sequence of the complete element is 1856 bp long and contains imperfect inverted terminal repeats (ITRs) of 53 bp. The target site duplication comprises the sequence TA. The amino acid sequence derived from one reading frame of Pat shows significant homology to members of the Fot1 family of transposons. However, this reading frame is interrupted by numerous stop codons. Since no transcripts of Pat were identified in different P. anserina strains grown under standard conditions and under increased stress, we conclude that none of the copies of Pat is active in the strains analyzed, under the environmental conditions investigated. Comparison of the sequences of the two cloned Pat sequences revealed 89% (589/747 nucleotides) identity. Most of the differences (82%, 129/158) can be attributed to transitions preferentially at CpA:TpG and CpT:ApG dinucleotides. The dinucleotide ratios in Pat are similar to those in a Neurospora crassa transposon which was subject to repeat-induced mutation (RIP), but differ significantly from those found in single-copy genes of P. anserina and in fungal DNA transposons not modified by this mechanism. Molecular analysis of the progeny of a cross between the wild-type strain and a transgenic strain in which a nuclear gene was duplicated by transformation yielded the first clear evidence that a RIP-like process is active in P. anserina.

Amino Acid Sequence↗
PubMed1997

Flipper, a mobile Fot1-like transposable element in Botrytis cinerea.

A transposable element, Flipper, was isolated from the phytopathogenic fungus Botrytis cinerea. The element was identified as an insertion sequence within the coding region of the nitrate reductase gene. The Flipper sequence is 1842 bp long with perfect inverted terminal repeats (ITRs) of 48 bp and an open reading frame (ORF) of 533 amino acids, potentially encoding for a transposase; the element is flanked by the dinucleotide TA. The encoded protein is very similar to the putative transposases of three elements from other phytopathogenic fungi, Fot1 from Fusarium oxysporum, and Pot2 and MGR586 from Magnaporthe grisea. The number of Flipper elements in strains of B. cinerea varied from 0 to 20 copies per genome. Analysis of the descendants of one cross showed that the segregation ratio of Flipper elements was 2:2 and that the copies were not linked.

Amino Acid Sequence↗
PubMed2006

Mobilization of a hobo-related sequence in the genome of Drosophila simulans.

The hobo transposable element can occur under three forms in the Drosophila genome: as a complete element (also called canonical), as internally deleted copies, or as hobo-related sequences (relics). Some evidence indicated that canonical elements and internally deleted copies are recent acquisitions of Drosophila genomes, while the "relics" are old components, normally degenerated and immobile. Here we present the characterization of a hobo-related sequence, found in the genome of a hypermutable strain of D. simulans, which insertion into the white locus raised a de novo white mutation. It is a shorter hobo related element presenting, overall, roughly 18% of divergence at the DNA level from the canonical hobo, with many indels that make clear this element is defective. However, its ITRs and flanking regions are extremely conserved. This is the first hobo "relic" showed to be mobilizable. We suggest, and point up some evidences, toward the idea that this sequence could have been mobilized by the canonical element. The presence of a similar "relic" element in D. sechellia allows us to suggest that these elements have been maintained mobilizable since the time of divergence between these species.

ATP-Binding Cassette Transporters↗
PubMed2007

First evidence of methylation in the genome of Drosophila willistoni.

DNA methylation has been studied abundantly in vertebrates and recent evidence confirms that this phenomenon could be disseminated among some invertebrates groups, including Drosophila species. In this paper, we used the Methylation-Sensitive Restriction Endonuclease (MSRE) technique and Southern blot with specific probes, to detect methylation in the Drosophila willistoni species. We found differential cleavage patterns between males and females that cannot be explained by Mendelian inheritance, pointing to a DNA methylation phenomenon different from the Drosophila melanogaster one. The sequencing of some of these bands showed that these fragments were formed by different DNA elements, among which rDNA. We also characterized the D. willitoni dDnmt2 sequence, through a Mega Blast search against the D. willistoni Trace Archive Database using the D. melanogaster dDnmt2 nucleotide sequence as query. The complete analysis of D. willistoni dDnmt2 sequence showed that its promoter region is larger, its dDnmt2 nucleotide sequence is 33% divergent from the D. melanogaster one, Inverted Terminal Repeats (ITRs) are absent and only the B isoform of the enzyme is produced. In contrast, ORF2 is more conserved. Comparing the D. willistoni and D. melanogaster dDnmt2 protein sequences, we found higher conservation in motifs from the large domain, responsible for the catalysis of methyl transfer, and great variability in the region that carries out the recognition of specific DNA sequences (TRD). Globally, our results reveal that methylation of the D. willistoni genome could be involved in a singular process of species-specific dosage compensation and that the DNA methylation in the Drosophila genus can have diverse functions. This could be related to the evolutionary history of each species and also to the acquisition time of the dDnmt2 gene.

Amino Acid Sequence↗
PubMedDate not supplied

Pilot study assessing TNF gene polymorphism as a prognostic marker for disease progression in neonates with sepsis.

In adult postoperative intensive care patients, the biallelic Ncol polymorphism within the tumor necrosis factor (TNF) locus has been shown to be a genomic marker for individuals with increased TNF-alpha response and poor prognosis in severe sepsis. We characterized the genomic distribution and allele frequency of the Ncol polymorphism in 23 preterm and term neonatal intensive care unit (NICU) patients with culture-proven sepsis and compared it with clinical and laboratory characteristics to assess its prognostic value for disease progression. Genotype analysis demonstrated the following absolute (relative) frequencies: 7 (0.31) infants were homozygous for the allele TNFB2 (Group A). 12 (0.52) infants were heterozygous (TNFB1/TNFB2) and four (0.17) infants homozygous for the allele TNFB1 (Group B). There was no significant difference compared to adult intensive care patients with severe sepsis (p = 0.31). The median gestational age of all infants (13 female and ten male) as well as for either group was 28 weeks (range 23-37) with a median birth weight of 845 g (range 560-2,720). The study population included a total of 16 very low birth weight (VLBW) infants, four in Group A and 12 in Group B. However, there was no significant difference for gestational age and birth weight in both groups (p = 0.82 and 0.71, respectively). Laboratory parameters as maximum and minimum leukocyte and thrombocyte counts, maximum immature to total neutrophil ratios (ITR), maximum C-reactive protein (CRP) levels, days of CRP levels > 5 mg/l and total days of antibiotic treatment, were not statistically different in both groups. In total, three infants (13%) died in consequence of their underlying disease. Two infants belonged to Group A and one to Group B. The statistical analysis of outcome variables (mortality, neurological impairment, failure to thrive) was not possible, because the study population was small and the reasons for poor outcome and death in these high-risk patients had to be considered multifactorial. In conclusion, in this pilot study the biallelic Ncol polymorphism within the TNF locus was not a prognostic marker for disease progression in high-risk NICU-admitted term and preterm infants with culture-proven sepsis. In order to detect differences in outcome similar to adult postsurgical patients with severe sepsis, an unfeasibly high number of NICU patients with culture-proven sepsis would need to be included for a similar study.

Adult↗
PubMed1985

Origin of adenovirus DNA replication. Role of the nuclear factor I binding site in vivo.

An assay is described that detects in vivo a single round of initiation and DNA synthesis directed by a linear molecule containing an exposed single copy of an adenovirus (Ad) origin of replication. This and a previously described assay, which measures multiple rounds of DNA replication, were used to identify DNA sequences within the Ad2 and Ad4 origins of replication that are important for ori function. Linear DNA molecules containing sequences from the Ad2 or Ad4 genome termini were cotransfected with homologous and heterologous helper virus, and net amounts of DNA synthesis were compared. Linear molecules containing the Ad4 inverted terminal repeats were replicated 20-fold better in the presence of the homologous helper, whereas both Ad2 and Ad4 inverted terminal repeats were utilized efficiently by Ad4. DNA sequence analysis of the Ad2 ori and the corresponding region in Ad4 indicated that, although there are only ten variant base-pairs, eight are located within the Ad2 DNA sequence recognized by the cellular protein nuclear factor I. This protein is required to achieve the maximal rate of Ad2 DNA replication in vitro, and these differences therefore identify DNA sequences that are crucial to Ad2 ori function. The Ad4 ITR does not contain a functional nuclear factor I binding site, and deletion analysis has demonstrated that this region of the Ad4 genome is not required for ori function. In contrast to Ad2, the DNA sequences required for the initiation of Ad4 DNA replication were shown to reside entirely within the terminal 18 base-pairs of the Ad4 inverted terminal repeat.

Adenoviridae↗
PubMed1990

High level expression of the envelope glycoproteins of the human immunodeficiency virus type I in presence of rev gene using helper-independent adenovirus type 7 recombinants.

The effect of rev (art/trs) gene on the level of HIV-1 envelope (env) expression using recombinant adenovirus was investigated. Recombinant adenoviruses expressing either the envelope or the rev gene of the human immunodeficiency virus type 1 (HIV-1) were constructed by inserting the gene into an expression cassette. The expression cassette contained the adenovirus type 7 major late promoter, followed by leader 1 of the adenovirus tripartite leader and a portion of intron between leaders 1 and 2, leaders 2 and 3, and a hexon polyadenylation signal. The cassette was then inserted at the terminal region between the E4 and ITR regions of the adenovirus 7 genome with a concomitant E3 region deletion (80-87 m.u.). A549 cells infected with the recombinant virus containing the env gene produced the envelope glycoproteins gp160, gp120, and gp41. HIV-1 envelope gene expression was greatly enhanced (20- to 50-fold) in the cells that were simultaneously infected with the recombinant adenovirus containing the rev gene as measured by ELISA and Western blotting. Interestingly, this effect was observed despite the lack of the 5' down splice site for rev and seems to be post-transcriptional. Another recombinant adenovirus which contains both the rev and the env genes was constructed by inserting the rev gene in the deleted E3 region and the env gene in the terminal cassette. This double recombinant virus expressed high levels of env antigen in A549 cells similar to those attained upon co-infection with two separate recombinant viruses containing the rev or env gene. Furthermore, the rev gene nucleotide sequence could be altered without altering the amino acid sequence and its sequences truncated by 17 amino acids from the C-terminus had no effect of rev function.

Adenoviridae↗
PubMed1985

Sequence of Dictyostelium DIRS-1: an apparent retrotransposon with inverted terminal repeats and an internal circle junction sequence.

The Dictyostelium discoideum transposon DIRS-1 contains long terminal repeats that are inverted (ITRs) and nonidentical. We show here that the internal sequence contains 4158 nucleotides and encodes three open reading frames (ORFs). Two of the ORFs (ORFs 2 and 3) are colinear and overlap for more than 2000 bases. Unusual sequence conservation between the two DIRS-1 elements in the overlap region is discussed. The conserved reading frame (ORF3) contains a 200 amino acid region that bears significant homology to retrovirus reverse transcriptase. Based on this homology, we classify DIRS-1 as a possible retrotransposon and propose a model by which the nearly genomic length 4.5 kb DIRS-1 RNA could be used to generate a genomic DNA copy of DIRS-1 with nonidentical inverted terminal repeats.

Base Sequence↗
PubMed2004

Short-form activity measure for post-acute care.

OBJECTIVE: To develop a comprehensive set of short forms using item response theory (IRT) and item pooling procedures for the purpose of monitoring postacute care functional recovery. DESIGN: Prospective study. SETTING: Six postacute health care networks in the greater Boston area, including inpatient acute rehabilitation, transitional care units, home care, and outpatient services. PARTICIPANTS: A convenience sample of 485 adult volunteers who were currently receiving skilled rehabilitation services. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: We developed a set of 6 short forms across 3 activity domains from new items and items from existing postacute care instruments. RESULTS: Inpatient- and community-based short forms were developed for each of 3 activity domains: physical & movement, applied cognition, and personal care & instrumental. Items were selected for inclusion on the short forms to maximize content coverage and information value of items across the range of content and to minimize ceiling and floor effects. We were able to match the distribution of sample scores with very good item precision for 1 of the constructs (physical & movement); the other 2 domains (personal care & instrumental, applied cognition) were more challenging because of the variability in patient recovery and ceiling effects. CONCLUSIONS: ITR methods and item pooling procedures were valuable in developing paired sets of short-form instruments for inpatient and community rehabilitation that provided estimates of functioning along a common metric for use across postacute care settings.

Activities of Daily Living↗
PubMed2006

Family of Tc1-like elements from fish genomes and horizontal transfer.

The involvement of horizontal transfer (HT) in the evolution of vertebrate transposable elements (TEs) is a matter of an ongoing debate. The phylogenetic relationships between Tc1 TEs, based on limited dataset have been previously used to infer a case of Tc1 HT between the genomes of fish and frogs. Here this hypothesis has been critically evaluated by the experimental approach including comparative data on the range of fish species available today. The distribution of a Tc1 subfamily of TE in selected fish species was investigated by PCR with a single primer complementary to ITRs and showed that they are widespread in the studied 17 fish species. They belong to five different subfamilies of Tc1 TEs, as revealed by the comparison with current genomic data for fish and amphibians. The original hypothesis would get much weaker support from the current data, although at least one novel potential and more convincing case of HT was identified between genomes of Perciformes fish. An interesting case of recombination-driven mobilisation of a degenerated TE by distantly related TE from different subfamily was discovered in the genome of pike. The occurrence of such cases widens the range of TE elements identifiable with the employed experimental approach. Further similar studies would help to explain the evolution of the multiple Tc1 lineages including species for which full genome sequences will not be available soon.

Animals↗
PubMed2004

A protein-protein binding assay using coated microtitre plates: increased throughput, reproducibility and speed compared to bead-based assays.

Protein-protein interactions, and the factors affecting them, are of fundamental importance to all biological systems. Surface plasmon resonance (SPR) and isothermal titration calorimetry (ITR) are powerful methods for assaying such interactions, but are expensive to implement. In contrast, bead-based pull-down assays using affinity tags such as glutathione-S-transferase (GST), require no specialist equipment. As a result, such assays are the most popular method for analysing protein-protein interactions, despite being time-consuming and prone to variability. In respect of these problems, we have modified this form of binding assay, using glutathione-coated 96-well plates rather than glutathione-Sepharose beads to bind the primary bait protein. Quantitation of bound protein utilises ELISA for purified proteins and scintillation counting for in vitro translated proteins, rather than the SDS-PAGE-based detection methods used in traditional bead-based assays. These modifications result in an approximately 10-fold increase in the number of samples that can be assayed daily, and allow results to be obtained within hours as opposed to days. We validate the modified assay by analysing the equilibrium binding of Munc18 and syntaxin, and also demonstrate that association and dissociation kinetics may be measured using this approach. The method we describe is generally applicable to any protein-protein interaction assay based on affinity tags and is amenable to automation, and so should benefit a wide range of biochemical research.

Automation↗