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Biomedical subjects

P Simonet

Publications and source records attributed to P Simonet.

At least 55 records · Page 3Linked to original sources
PubMed1992

The nodular endophytes of Coriaria spp. form a distinct lineage within the genus Frankia.

Repeated attempts at isolating the Frankia endophyte of Coriaria spp. have not yielded infective microbial cultures that could fulfil Koch's postulates. In order to circumvent the critical isolation step, nodule endophytes of Coriaria were characterized directly by means of specific amplification of nodule DNA (PCR) followed by sequencing of part of the 16S rDNA gene. Three closely related sequences were obtained from nodules originating from France, Mexico and New Zealand, containing unique sequences different from all other Frankia strains characterized so far. The sequences obtained were closest (with 5 or 6 substitutions) to those of Frankia alni and those of Casuarina-infective Frankia strains, respectively. Two nucleotides unique to the Coriaria endophyte sequences were used to define specific primers, resulting in a hybridization test that could discriminate between Frankia DNAs originating from Coriaria nodules and those recovered from all cultured Frankia strains tested. The endophytes of Coriaria thus appear to form a distinct Frankia lineage.

Actinomycetales↗
PubMed1992

Evidence that some Frankia sp. strains are able to cross boundaries between Alnus and Elaeagnus host specificity groups.

Phenotypic and genotypic methods were used to prove the existence of Frankia strains isolated from an Elaeagnus sp. that are able to cross the inoculation barriers and infect Alnus spp. also. Repeated cycles of inoculation, nodulation, and reisolation were performed under axenic conditions. Frankia wild-type strain UFI 13270257 and three of its coisolates did exhibit complete infectivity and effectiveness on Elaeagnus spp. and Hippophaë rhamnoides and variable infectivity on Alnus spp. Microscopical observation of host plant roots showed that these strains are able to infect Alnus spp. by penetrating deformed root hairs. Reisolates obtained from nodules induced on monoxenic Alnus glutinosa, Alnus incana, and Elaeagnus angustifolia resembled the parent strains in host infectivity range, in planta and in vitro morphophysiology, isoenzymes, and nif and rrn restriction fragment length polymorphisms, thus fulfilling Koch's postulates on both host plant genera. Alnus and Elaeagnus group-specific polymerase chain reaction DNA amplifications, DNA-DNA hybridizations, and partial gene sequences coding for 16S rRNA provided evidence for the genetic uniformity of wild-type strains and their inclusion into one and the same genomic species, clearly belonging to the Elaeagnus group of Frankia species.

Actinomycetales↗
PubMed1992

Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction.

In order to develop a rapid and specific detection test for bacteria in soil, we improved a method based on the polymerase chain reaction (PCR). Each step of the protocol, including direct lysis of cells, DNA purification, and PCR amplification, was optimized. To increase the efficiency of lysis, a step particularly critical for some microorganisms which resist classical techniques, we used small soil samples (100 mg) and various lytic treatments, including sonication, microwave heating, and thermal shocks. Purification of nucleic acids was achieved by passage through up to three Elutip d columns. Finally, PCR amplifications were optimized via biphasic protocols using booster conditions, lower denaturation temperatures, and addition of formamide. Two microorganisms were used as models: Agrobacterium tumefaciens, which is naturally absent from the soil used and was inoculated to calibrate the validity of the protocol, and Frankia spp., an actinomycete indigenous to the soil used. Specific primers were characterized either in the plasmid-borne vir genes for A. tumefaciens or in the variable regions of the 16S ribosomal gene for Frankia spp. Specific detection of the inoculated A. tumefaciens strain was routinely obtained when inocula ranged from 10(7) to 10(3) cells. Moreover, the strong correlation we observed between the size of the inocula and the results of the PCR reactions permitted assessment of the validity of the protocol in enumerating the number of microbial cells present in a soil sample. This allowed us to estimate the indigenous population of Frankia spp. at 0.2 x 10(5) genomes (i.e., amplifiable target sequences) per g of soil.

Agrobacterium tumefaciens↗
PubMed1991

Frankia genus-specific characterization by polymerase chain reaction.

The polymerase chain reaction (PCR) is an in vitro procedure for primer-directed enzymatic amplification of specific template nucleic acid sequences. In order to determine whether a given actinomycete isolated from an actinorhiza (nodule) belongs to the genus Frankia or is a contaminant, we have developed a test based on the PCR. Primers complementary to sequences of two DNA regions corresponding to the nif genes (nifH and nifD) and the rRNA genes (16S and 23S) were specifically chosen to differentially amplify DNAs from Frankia strains but not those from other microorganisms. A series of positive and negative controls were set up by using universal or selective primers resulting in a discriminant amplification, which could be detected after agarose gel electrophoresis. In the nif region, degenerate oligonucleotide primers were used to amplify a target common to all the nitrogen-fixing microorganisms tested, while another set of primers amplified a target with a high specificity for Frankia strains. In the rRNA gene region, universal and specific primers were characterized and tested with DNAs from a wide range of microorganisms. The efficiency of this rapid and sensitive PCR assay was tested with an isolate obtained from Alnus nepalensis nodules, confirming results obtained by nodulation tests.

Actinomycetales↗
PubMed1991

Phylogenetic relationships among Frankia genomic species determined by use of amplified 16S rDNA sequences.

Actinomycetes of the genus Frankia establish a nitrogen-fixing symbiosis with a large number of woody dicotyledonous plants. Hundreds of strains isolated from various actinorhizal plants growing in different geographical areas have recently been classified into at least nine genomic species by use of the DNA-DNA hybridization technique (M.P. Fernandez, H. Meugnier, P.A.D. Grimont, and R. Bardin, Int. J. Syst. Bacteriol. 39:424-429, 1989). A protocol based on the amplification and sequencing of 16S ribosomal DNA segments was used to classify and estimate the phylogenetic relationships among eight different genomic species. A good correlation was established between the grouping of strains according to their 16S ribosomal DNA sequence homology and that based on total DNA homology, since most genomic species could be characterized by a specific sequence. The phylogenetic tree showed that strains belonging to the Alnus infectivity group are closely related to strains belonging to the Casuarina infectivity group and that strains of these two infectivity groups are well separated from strains of the Elaeagnus infectivity group, which also includes atypical strains isolated from the Casuarina group. This phylogenetic analysis was also very efficient for classifying previously unclassified pure cultures or unisolatable strains by using total DNA extracted directly from nodules.

Actinomycetales↗
PubMed1990

Identification of Frankia strains in nodules by hybridization of polymerase chain reaction products with strain-specific oligonucleotide probes.

A set of oligonucleotides has been developed to study the competitivity of two Frankia strains in the nodulation of the roots of two host plant species: Alnus glutinosa and Alnus incana. Two 20 mer-oligonucleotides, complementary to highly conserved sequences inside the nifH gene, were used as primers for the polymerase chain reaction (PCR) system in order to amplify microsymbiont DNA extracted from actinorhizae. PCR products were analyzed using two strain-specific 15-mer oligonucleotides identified in the amplified region. Hybridization data indicate that strain ACoN24d is more competitive than strain ArI3 in the nodulation of both hosts.

Actinomycetales↗
PubMed1990

The optical transverse chromatic aberration on the fovea of the human eye.

The horizontal component of optical transverse chromatic aberration (TCA) at the fovea between 486 and 656 nm is measured in a sample of 8 eyes by two novel methods, both using vernier adjustment tasks with a retinal illumination of approx. 780 td and for a pupil size of approximately 5.5 mm dia. Initially, in an indirect method, TCA is derived along the line of sight from chromatic parallax. Secondly, TCA is measured directly using a semi-Maxwellian view and compensating for longitudinal chromatic aberration (LCA). Both techniques are unaffected by coma or by the Stiles-Crawford effects, thus optical TCA rather than the TCA perceived in normal view is measured. On average, optical TCA is in the same direction but less than previously predicted by eye models and predictions of the optical quality of the eye in white light are modified. Factors underlying the lower average value of optical TCA and variability among subjects, especially pupil centration and foveal position, are discussed. The relationship of optical TCA to TCA perceived in normal view and to chromostereopsis is analysed. The results suggest that the optical design of the human eye is optimized to reduce the wavelength dependent phase shift in the optical transfer function, which could be produced by optical TCA.

Accommodation, Ocular↗
PubMed1990

Psychophysical measurement of the blur on the retina due to optical aberrations of the eye.

The blur on the retina in the horizontal meridian due to monochromatic and chromatic aberrations has been measured using a novel psychophysical technique. Longitudinal chromatic aberration gives the dominant blur for pupil sizes of 4-5 mm, followed by monochromatic aberrations, and blur due to optical transverse chromatic aberration. In some eyes, coma was present as a result of a displacement of the axis of symmetry from the centre of the pupil, but in three eyes, coma was present without spherical aberration. The technique also allows a measurement of the effective pupil centre relative to the geometric centre and a partial analysis of the relative positions of the reference axes of the eye.

Adolescent↗
PubMed1990

Effect of illuminance on the directions of chromostereopsis and transverse chromatic aberration observed with natural pupils.

The direction of chromostereopsis observed with a natural pupil and the direction of the monocularly perceived disparity between coloured targets (F and C lines - 486 and 656 nm) have been measured in a sample of 30 subjects at 10 and 1000 lx. At both illumination levels approximately equal numbers of subjects perceived positive and negative chromostereopsis. When the ambient illumination was increased, a reversal in the direction of the chromostereopsis occurred for 16 subjects. For six of them a change from a positive to a negative chromostereopsis was observed, a pattern not reported in previous studies. In most cases at both high and low illuminance, there was an absence of perception of a monocular disparity (transverse chromatic aberration), although chromostereopsis was reported, indicating that binocular information can be obtained from sub-threshold monocular disparities. At low illuminance, the lack of correlation between the direction of chromostereopsis and transverse chromatic aberration (TCA) may indicate that there may be a supplementary binocular factor in chromostereopsis.

Adult↗
PubMed1988

Conservation of nif sequences in Frankia.

Southern blots of Frankia total DNAs were hybridized with nifHDK probes from Rhizobium meliloti, Klebsiella pneumoniae and Frankia strain Arl3. Differences between strains were noted in the size of the hybridizing restriction fragments. These differences were more pronounced among Elaeagnus-compatible strains than among Alnus- or Casuarina-compatible strains. Gene banks constructed for Frankia strains EUN1f, HRN18a, CeD and ACoN24d were used to isolate nif-hybridizing restriction fragments for subsequent mapping and comparisons. The nifH zone had the highest sequence conservation and the nifH and nifD genes were found to be contiguous. The complete nucleotide sequence of the nifH open reading frame (ORF) from Frankia strain Arl3 is 861 bp in length and encodes a polypeptide of 287 amino acids. Comparisons of these nucleic acid and amino acid sequences with other published nifH sequences suggest that Frankia is most similar to Anabaena and Azotobacter spp. and K. pneumoniae and least similar to the Gram-positive Clostridium pasteurianum and to the archaebacterium Methanococcus voltae.

Actinomycetales↗
PubMed1988

Identification of frankia strains by direct DNA hybridization of crushed nodules.

A hybridization procedure was developed to identify Frankia strains inside actinorhizae by direct probing of crushed root nodules. The probe consisted of an indigenous cryptic plasmid. This well-conserved, 8-kilobase plasmid was detected in Frankia isolates that were very close taxonomically (they possessed a very high DNA sequence homology). The probe did not hybridize to the DNA of Frankia isolates which did not carry the plasmid. Endophyte DNA was extracted by a modification of a technique originally developed for the detection of plasmids in Frankia isolates. The hybridization procedure applied to nodules collected in a stand of alder permitted determination of a distribution map of the plasmid-bearing Frankia strains.

Journal Article↗
PubMed1986

Peripheral power variations in progressive addition lenses.

The peripheral powers were studied in two types of progressive addition lenses: the AO Ultravue 28 and the Essilor Varilux 2. The marginal dioptric power was measured with respect to the vertex sphere with a device adapted to a Nikon projection vertexometer. The graphical representation of the results permits the power variations to be evaluated rapidly. The results demonstrate some optical characteristics of each of the lenses. Thus it is possible to establish a ratio between the peripheral astigmatism and the addition. The angular area of astigmatic zones could also be estimated.

Astigmatism↗
PubMed1984

[Power in the periphery of several aspheric eyeglasses for aphakic patients].

A special device adapted to a Nikon projection vertexometer permits the power to be measured in the periphery of recent aspheric aphakic lenses. The peripheral power is measured with respect to the vertex sphere. A blended lenticular aspheric lens and three types of zonal aspheric full field lenses are studied, with various base curves on three samples. Four meridians of each lens are evaluated with ocular rotations varying by 5 degrees step up to 35 degrees at least. The results show a variable oblique astigmatism and a high under-correction of the mean oblique power for the Welsh 4 drop. The other zonal aspheric lenses give only a slight improvement of the peripheral powers compared with some conventional aspheric lenses. The Omega lens shows a reasonable correction of off-axis power errors up to 30 degrees. Beyond, the powers variation follows the general characteristics of blended lenticular aspheric lenses.

Aphakia, Postcataract↗
PubMed1983

Plasmids in Frankia sp.

A method to achieve cell lysis and isolate Frankia sp. plasmid DNA was developed. A screening of Frankia sp. strains belonging to different host compatibility groups (Alnus sp., Elaeagnus sp., Ceanothus sp.) showed that, of 39 strains tested, 4 (strains Cp11, ARgN22d, ArI3, and EUN1f) possessed plasmids ranging in size from 7.1 to 32.2 kilobase pairs as estimated from agarose gel electrophoresis and electron microscopy. A total of 11 plasmids were detected.

Actinomycetales↗
PubMed1983

A scanning focimeter to measure peripheral lens powers.

A special device adapted to a Nikon projection vertexometer permits the power to be measured in the periphery of ophthalmic lenses. The marginal power can be measured with respect to the vertex sphere. Various values of the vertex sphere radius can be obtained with this instrument. The characteristics of this modified focimeter are described in this paper.

Eyeglasses↗