Distribution dynamics of the Tnt1 retrotransposon in tobacco

Retrotransposons contribute significantly to the size, organization and genetic diversity of plant genomes. Although many retrotransposon families have been reported in plants, to this day, the tobacco Tnt1 retrotransposon remains one of the few elements for which active transposition has been shown. Demonstration that Tnt1 activation can be induced by stress has lent support to the hypothesis that, under adverse conditions, transposition can be an important source of genetic variability. Here, we compared the insertion site preference of a collection of newly transposed and pre-existing Tnt1 copies identified in plants regenerated from protoplasts or tissue culture. We find that newly transposed Tnt1 copies are targeted within or close to host gene coding sequences and that the distribution of pre-existing insertions does not vary significantly from this trend. Therefore, in spite of their potential to disrupt neighboring genes, insertions within or near CDS are not preferentially removed with age. Elimination of Tnt1 insertions within or near coding sequences may be relaxed due to the polyploid nature of the tobacco genome. Tnt1 insertions within or near CDS are thus better tolerated and can putatively contribute to the diversification of tobacco gene function. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Tuning of the enzyme ratio in a neutral redox convergent cascade: A key approach for an efficient one-pot/two-step biocatalytic whole-cell system

The efficiency of a versatile in vivo cascade involving a promiscuous alcohol dehydrogenase, obtained from a biodiversity search, and a Baeyer–Villiger monooxygenase was enhanced by the independent control of the production level of each enzyme to produce ε-caprolactone and 3,4-dihydrocoumarin. This goal was achieved by adjusting the copy number per cell of Escherichia coli plasmids. We started from the observation that this number generally correlates with the amount of produced enzyme and demonstrated that an in vivo multi-enzymatic system can be improved by the judicious choice of plasmid, the lower activity of the enzyme that drives the limiting step being counter-balanced by a higher concentration. Using a preconception-free approach to the choice of the plasmid type, we observed positive and negative synergetic effects, sometimes unexpected and depending on the enzyme and plasmid combinations. Experimental optimization of the culture conditions allowed us to obtain the complete conversion of cyclohexanol (16 mM) and 1-indanol (7.5 mM) at a 0.5-L scale. The yield for the conversion of cyclohexanol was 80% (0.7 g ε-caprolactone, for the productivity of 244 mg·L ⁻¹·h ⁻¹) and that for 1-indanol 60% (0.3 g 3,4-dihydrocoumarin, for the productivity of 140 mg·L ⁻¹·h ⁻¹).     

Zinc tolerance and hyperaccumulation are genetically independent characters

The hyperaccumulation of metals by a rare class of plants is a fascinating and little understood phenomenon. No genetic analysis has been possible since no intraspecific variation is known for this character. Here, we report on crosses between the zinc-hyperaccumulating and -tolerant species Arabidopsis halleri and the non-hyperaccumulating, non-tolerant species Arabidopsis petraea. The F2 segregates for both characters and it appears that the two characters are genetically independent. The data for tolerance are consistent with a single major gene for this character (although the number of genes for hyperaccumulation cannot be determined), and is probably not very large.     

Elimination of extrachromosomal c-myc genes by hydroxyurea induces apoptosis

Hydroxyurea (HU) increases extrachromosomal DNA elimination in tumor cell lines. The c-myc oncogene is one of the many relevant amplified genes contained within the extrachromosomal DNA compartment. Spontaneous loss of amplified copies of c-myc induces terminal differentiation and apoptosis in the human HL-60 leukemia cell lines. In the present study, we evaluate HU's ability to induce apoptosis by eliminating extrachromosomally located c-myc oncogene in human tumor cell lines. The consequences of eliminating extrachromosomal DNA by HU were explored in two different cell lines using the TdT assay and acridine orange/ethidium bromide labeling. COLO 320 clone 3 and COLO 320 clone 21 cell lines contain the same number of amplified copies of c-myc oncogene, but located respectively on extrachromosomal DNA, and intrachromosomally in homogeneously staining regions. HU induced apoptosis in the COLO 320 clone 3 cell line by a time and concentration dependent mechanism but could not induce apoptosis in the COLO 320 clone 21 cell line. These results suggested that HU-induced apoptosis in COLO 320 cell lines depends on elimination of extrachromosomal amplified copies of the c-myc oncogene. The ability of HU to eliminate extrachromosomally amplified copies of the c-myc oncogene and to induce apoptosis should be considered when targeting malignancies with amplification of the c-myc oncogene in an extrachromosomal site.     

Hereditary deafness: molecular genetics

This article outlines recent advances in explaining hereditary deafness in molecular terms, focusing on isolated (i.e. nonsyndromic) hearing loss. The number of genes identified (36 to date) is growing rapidly. However, difficulties inherent in genetic linkage analysis, coupled with the possible involvement of environmental causes, have so far prevented the characterization of the main genes causative or predisposing to the late-onset forms of deafness.     

Face transplantation: where do we stand?

The recent clinical cases of hand and composite tissue allotransplantation opened a new era in the practice of reconstructive surgery. Some have suggested that face (allo)transplantation could be the next step to benefit patients whose conditions cannot be addressed by conventional techniques of reconstructive surgery using autologous tissues. This article reviews the current status of science regarding the prospect of human face transplantation. The main issues fall into three categories: (1) the surgical challenge of the procedure, specifically regarding vascular viability and functional recovery of the graft; (2) the risks of side effects from life-long immunosuppression necessary to prevent graft rejection; and (3) the ethical debate and the effects of the procedure on the population. Although face transplantation could one day be performed and extend the boundaries of reconstructive surgery, there are currently many obstacles that need to be overcome first.     

A novel locus for autosomal dominant nonsyndromic hearing loss (DFNA44) maps to chromosome 3q28–29

Hereditary non-syndromic sensorineural hearing loss (NSSHL) is a genetically highly heterogeneous group of disorders. Autosomal dominant forms account for up to 20% of cases. To date, 39 loci have been identified by linkage analysis of affected families that segregate NSSHL forms in the autosomal dominant mode (DFNA). Investigation of a large Spanish pedigree with autosomal dominant inheritance of bilateral and progressive NSSHL of postlingual onset excluded linkage to known DFNA loci and, in a subsequent genome-wide scan, the disorder locus was mapped to 3q28-29. A maximum two-point LOD score of 4.36 at theta=0 was obtained for marker D3S1601. Haplotype analysis placed the novel locus, DFNA44, within a 3-cM genetic interval defined by markers D3S1314 and D3S2418. Heteroduplex analysis and DNA sequencing of coding regions and exon/intron boundaries of two genes (CLDN16 and FGF12) in this interval did not reveal disease-causing mutations.     

Biomechanical modeling of posterior instrumentation of the scoliotic spine

Scoliosis is a three-dimensional deformation of the spine that can be treated by vertebral fusion using surgical instrumentation. However, the optimal configuration of instrumentation remains controversial. Simulating the surgical maneuvers with personalized biomechanical models may provide an analytical tool to determine instrumentation configuration during the pre-operative planning. Finite element models used in surgical simulations display convergence difficulties as a result of discontinuities and stiffness differences between elements. A kinetic model using flexible mechanisms has been developed to address this problem, and this study presents its use in the simulation of Cotrel-Dubousset Horizon surgical maneuvers. The model of the spine is composed of rigid bodies corresponding to the thoracic and lumbar vertebrae, and flexible elements representing the intervertebral structures. The model was personalized to the geometry of three scoliotic patients (with a thoracic Cobb angle of 45 degrees, 49 degrees and 39 degrees ). Binary joints and kinematic constraints were used to represent the rod-implant-vertebra joints. The correction procedure was simulated using three steps: (1) Translation of hooks and screws on the first rod; (2) 90 degrees rod rotation; (3) Hooks and screws look-up on the rod. After the simulation, slight differences of 0-6 degrees were found for the thoracic spine scoliosis and the kyphosis, and of 1-8 degrees for the axial rotation of the apical vertebra and for the orientation of the plane of maximum deformity, compared to the real post-operative shape of the patient. Reaction loads at the vertebra-implant link were mostly below 1000 N, while reaction loads at the boundary conditions (representing the overall action of the surgeon) were in the range 7-470 N and maximum torque applied to the rod was 1.8 Nm. This kinetic modeling approach using flexible mechanisms provided a realistic representation of the surgical maneuvers. It may offer a tool to predict spinal geometry correction and assist in the pre-operative planning of surgical instrumentation of the scoliotic spine.     

The human polycomb group EED protein interacts with the integrase of human immunodeficiency virus type 1

Human EED, a member of the superfamily of WD-40 repeat proteins and of the Polycomb group proteins, has been identified as a cellular partner of the human immunodeficiency virus type 1 (HIV-1) matrix (MA) protein (R. Peytavi et al., J. Biol. Chem. 274:1635-1645, 1999). In the present study, EED was found to interact with HIV-1 integrase (IN) both in vitro and in vivo in yeast. In vitro, data from mutagenesis studies, pull-down assays, and phage biopanning suggested that EED-binding site(s) are located in the C-terminal domain of IN, between residues 212 and 264. In EED, two putative discrete IN-binding sites were mapped to its N-terminal moiety, at a distance from the MA-binding site, but EED-IN interaction also required the integrity of the EED last two WD repeats. EED showed an apparent positive effect on IN-mediated DNA integration reaction in vitro, in a dose-dependent manner. In situ analysis by immunoelectron microscopy (IEM) of cellular distribution of IN and EED in HIV-1-infected cells (HeLa CD4(+) cells or MT4 lymphoid cells) showed that IN and EED colocalized in the nucleus and near nuclear pores, with maximum colocalization events occurring at 6 h postinfection (p.i.). Triple colocalizations of IN, EED, and MA were also observed in the nucleoplasm of infected cells at 6 h p.i., suggesting the ocurrence of multiprotein complexes involving these three proteins at early steps of the HIV-1 virus life cycle. Such IEM patterns were not observed with a noninfectious, envelope deletion mutant of HIV-1.