Biomedical subjects

H T Nguyen

Publications and source records attributed to H T Nguyen.

At least 37 records · Page 2Linked to original sources

PubMed2004

New investigation on the tetragonal liquid-crystalline phase or SmQ.

Chiral liquid crystals, for which twist and smectic order strongly compete, can exhibit complex architectures. This is the case of the SmQ phase which shows a high degree of 3D order (tetragonal or hexagonal) as well as a liquid signature. We have combined X-ray scattering and optical observations on a new compound exhibiting a SmQ phase to discriminate between the two models proposed by A.M. Levelut et al. (J. Phys. II 7, 981 (1997)) at the molecular level for the phase with the I4(1)22 space group.

Journal Article↗

PubMed2004

Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map.

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5' and 3' sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics.

Blotting, Southern↗

PubMed2004

Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.).

A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAM W101, BH1146, Butte 86), tetraploid durum wheat (T. turgidum L.), diploid wheat (T. monococcum L.), and two other diploid members of the grass tribe Triticeae (Aegilops speltoides Tausch and Secale cereale L.). The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags (ESTs) were examined by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAP3. Following these processing steps, this assembly yielded 101,107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 "unigenes." Analysis of the distribution of these unigenes among the libraries led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature.

Expressed Sequence Tags↗

PubMed2004

Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis.

A total of 944 expressed sequence tags (ESTs) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat (Triticum aestivum L.). EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and 1D with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences (E < or = e(-10)), where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses.

Arabidopsis↗

PubMed2004

A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice.

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.

Chromosome Mapping↗

PubMed2004

Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1.

The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags (ESTs) accounting for 2266 restriction fragments (loci) on the homoeologous group 3 chromosomes of hexaploid wheat (Triticum aestivum L.). Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology (GO) classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 (44%) of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes approximately 21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected.

Chromosome Mapping↗

PubMed2004

Analysis of expressed sequence tag loci on wheat chromosome group 4.

A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes (ESTs) from 26 Triticeae cDNA libraries, were mapped to wheat (Triticum aestivum L.) homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes, while 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions, previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoeologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology (only 26 of the 119 consensus ESTs) was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases.

Chromosome Mapping↗

PubMed2004

A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice.

We constructed high-density deletion bin maps of wheat chromosomes 5A, 5B, and 5D, including 2338 loci mapped with 1052 EST probes and 217 previously mapped loci (total 2555 loci). This information was combined to construct a consensus chromosome bin map of group 5 including 24 bins. A relatively higher number of loci were mapped on chromosome 5B (38%) compared to 5A (34%) and 5D (28%). Differences in the levels of polymorphism among the three chromosomes were partially responsible for these differences. A higher number of duplicated loci was found on chromosome 5B (42%). Three times more loci were mapped on the long arms than on the short arms, and a significantly higher number of probes, loci, and duplicated loci were mapped on the distal halves than on the proximal halves of the chromosome arms. Good overall colinearity was observed among the three homoeologous group 5 chromosomes, except for the previously known 5AL/4AL translocation and a putative small pericentric inversion in chromosome 5A. Statistically significant colinearity was observed between low-copy-number ESTs from wheat homoeologous group 5 and rice chromosomes 12 (88 ESTs), 9 (72 ESTs), and 3 (84 ESTs).

Chromosome Mapping↗

PubMed2004

Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags.

To localize wheat (Triticum aestivum L.) ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions (bins) flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs, 2043 (loci) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin.

Chromosome Mapping↗

PubMed2004

A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7.

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.

Chromosome Mapping↗

PubMed2004

A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat.

Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.

Chromosome Mapping↗

PubMed2003

Mapping osmotic adjustment in an advanced back-cross inbred population of rice.

Osmotic adjustment is one of several characters putatively associated with drought tolerance in rice. Indica cultivars are known to have a greater capacity for osmotic adjustment than japonica cultivars. We developed an advanced back-cross population using an indica donor, IR62266-42-6-2, to introgress osmotic adjustment into an elite japonica cultivar, IR60080-46A. One hundred and fifty BC(3)F(3) families were genotyped using microsatellites and RFLP markers, and a few candidate genes. We evaluated osmotic adjustment in these lines under greenhouse conditions using the re-hydration technique. Using the composite interval mapping technique, we detected 14 QTLs located on chromosomes 1, 2, 3, 4, 5, 7, 8 and 10 that together explained 58% of the phenotypic variability. Most, but not all, of the alleles with positive effects came from the donor parent. On chromosome 8, two QTLs were associated in repulsion. The QTL locations were in good agreement with previous studies on this trait on rice and in other cereals. Some BC(3)F(3) lines carried the favorable alleles at the two markers flanking up to four QTLs. Intercrossing these lines followed by marker-aided selection in their progenies will be necessary to recover lines with levels of osmotic adjustment equal to the donor parent. The advanced back-cross strategy appeared to be an appropriate method to accelerate the process of introgressing interesting traits into elite material.

Adaptation, Psychological↗

PubMed2003

Diagnostic abilities of three CAD methods for assessing microcalcifications in mammograms and an aspect of equivocal cases decisions by radiologists.

Radiologists use an "Overall impression" rating to assess a suspicious region on a mammogram. The value ranges from 1 to 5. They will definitely send a patient for biopsy if the rating is 4 or 5. They will send the patient for core biopsy when a rating of 3 (indeterminate) is given. We have developed three methods to aid diagnosis of cases with microcalcifications. The first two methods, namely, Bayesian and multiple logistic regression (with a special "cutting score" technique), utilise six parameter ratings which minimise subjectivity in characterising the microcalcifications. The third method uses three parameters (age of patient, uniformity of size of microcalcification and their distribution) in a multiple stepwise regression. For both training set and test set, all three methods are as good as the two radiologists in terms of percentages of correct classification. Therefore, all three proposed methods potentially can be used as second readers.

Algorithms↗

PubMed2003

Switching of banana liquid crystal mesophases under field.

Taking advantage of the great number of bent-core or "banana" compounds synthesized and studied in the laboratory, we describe their behaviour under the application of an external electric field. If the field were a static one, we would work within the frame of an equilibrium phase diagram in a (field E, temperature T) space where some phases would be simple dielectrics and others ferroelectric ones with a macroscopic polarization, either spontaneous or induced by the field. In this paper, we deal with the basic responses of "banana" liquid crystals under the application of a low frequency (1 to 100 Hz) AC field. Firstly square-wave voltages allow us to locate the phase boundary between dielectric (at lower field) and ferroelectric phases (higher field) at a given temperature and field threshold. Then we apply slowly varying AC voltages with shapes like triangle or "triple-plateau" to check out the stability of the induced ferroelectric phase versus field removal. Three behaviours are encountered, the unstable one (short lifetime of the high-field ferroelectric phase) where the macroscopic polarization is destroyed and then rebuilt in the opposite direction during each half period and usually called "antiferroelectric"; the stable one (long lifetime) with a polarization that rotates at constant modulus which is labeled as "ferroelectric" and a new one where the macroscopic polarization is proportional to the applied field, we named this behaviour as "superparaelectric". Let us stress that these observations apply to the ferroelectric phases of the (E, T) phase diagram not to the zero field (0,T) phases observed in the usual phase characterization experiments except for an eventual spontaneous ferroelectric phase.

Journal Article↗

PubMed2003

Rectangular to hexagonal columnar phase transition exhibited by a biforked mesogen.

We present the structural study of a biforked compound exhibiting a Colr-Colh phase transition. This study was performed by means of DSC, optical microscopy, X-ray diffraction, dilatometry and molecular modelling. The molecular packing within the two columnar mesophases of this compound is discussed. For the first time, it is shown that the clusters of adjacent molecules which form the elementary section of a column are tilted with respect to the columnar axis in the rectangular mesophase. From the whole set of experimental data, the number of molecules in a columnar section is found to be about 5 in the rectangular mesophase, and 4 in the hexagonal one. The transition between the two columnar mesophases is discussed with respect to its slow kinetics.

Journal Article↗

PubMed2003

Textural analysis of a mesophase with banana shaped molecules.

Observed under the polarizing microscope, the B7bis phase in the banana compound D14F3 [J.P. Bedel et al., Liq. Cryst. 27, 1411 (2000)] displays two types of textures of defects, namely (a): helical ribbons, that nucleate in large quantities when the samples are quenched from a sufficiently high temperature in the isotropic phase (b)- shapes with no helicity having the structure of developable domains much akin to those observed in columnar phases, either resulting from the annealing of the helical ribbons or nucleating under slow cooling processes. The existence of these two kinds of defects points toward the complex nature of the structure of the B7 phase, which is at the same time a columnar and a smectic phase. Our observations fit the model [M. Kleman, J. Phys. France 46, 1193 (1985)] according to which the geometry of a helical ribbon is that one of the central region of a screw dislocation with a giant Burgers vector, split into two helical disclination lines of strength k = 1/2 which bound the ribbon. Textures and defects, already partly documented, and growth features and annealing processes, not yet reported in the literature, are analyzed. We conclude that the helical ribbons and the developable domains with no helicity are textures of two different B7 states, namely a metastable state and the ground state respectively. Comparative textural analysis is performed for two other banana compounds exhibiting B2 phases.

Journal Article↗

PubMed2003

Self-organization of N() inclusions in SmC() free-standing films.

The behaviour of freely suspended smectic-C* ( SmC(*)) films at the bulk SmC(*)-cholesteric ( N(*)) phase transition has been investigated using polarized-reflected-light microscopy. Our experimental observations show that above the bulk SmC(*)- N(*) phase transition the N(*) order appears in different ways according to the film thickness. In thin films, the conventional layer-by-layer thinning occurs. In films of intermediate thickness N(*) inclusions nucleate inside the SmC(*) film. The distortions of the in-plane orientational order of the SmC(*) host phase induce elastic interactions between the inclusions and lead to their self-organization in chain-like structures. Both the dynamic of the chaining and the parameters driving the equilibrium distance between the inclusions in the chain are investigated. In thick films, N(*) fingers grow inside the film. The influence of the experimental conditions on the various processes is analysed.

Journal Article↗

PubMed2002

Mapping of genes controlling aluminum tolerance in rice: comparison of different genetic backgrounds.

Aluminum toxicity is the main factor limiting the productivity of crop plants in acid soils, particularly in the tropics and subtropics. In this study, a doubled-haploid population derived from the rice ( Oryza sativa L.) breeding lines CT9993 and IR62266 was used to map genes controlling Al tolerance. A genetic linkage map consisting of 280 DNA markers (RFLP, AFLP and SSR) was constructed to determine the position and nature of quantitative trait loci (QTLs) affecting Al tolerance. Three characters - control root length (CRL), Al-stressed root length (SRL) and root length ratio (RR) - were evaluated for the DH lines and the parents at the seedling stage in nutrient solution. A total of 20 QTLs controlling root growth under Al stress and control conditions were detected and distributed over 10 of the 12 rice chromosomes, reflecting multigenic control of these traits. The two QTLs of largest effect, qALRR-1-1 and qALRR-8 for root length ratio (a measurement of Al tolerance) were localized on chromosomes 1 and 8, respectively. Three other QTLs in addition to qALRR-8 were apparently unique in the CT9993 x IR62266 mapping population, which may explain the high level of Al tolerance in CT9993. Comparative mapping identified a conserved genomic region on chromosome 1 associated with Al tolerance across three rice genetic backgrounds. This region provides an important starting point for isolating genes responsible for different mechanisms of aluminum tolerance and understanding the genetic nature of this trait in rice and other cereals.

Aluminum↗