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J D Thompson

Publications and source records attributed to J D Thompson.

At least 55 records · Page 3Linked to original sources
PubMed2001

Engraftment of DLA-haploidentical marrow with ex vivo expanded, retrovirally transduced cytotoxic T lymphocytes.

Genetically modified donor T cells with an inducible "suicide" gene have the potential to improve the safety and availability of allogeneic hematopoietic stem cell transplantation by enhancing engraftment and permitting control of graft-versus-host disease (GVHD). However, several clinical studies of gene-modified T cells have shown limited to no in vivo function of the ex vivo expanded T cells. Using the well-established dog model of allogeneic marrow transplantation, the question was asked if retrovirally transduced, donor derived, ex vivo expanded cytotoxic T lymphocytes (CTLs) that are recipient specific could enhance engraftment of dog leukocyte antigen (DLA)-haploidentical marrow following a single dose of 9.2 Gy total body irradiation and no postgrafting immunosuppression. In this setting, only 4 of 11 control recipients of DLA-haploidentical marrow without added CTLs engrafted. CTLs did not enhance engraftment of CD34(+) selected peripheral blood stem cells. However, recipient-specific CTLs enhanced engraftment of DLA-haploidentical marrow in 9 of 11 evaluable recipients (P =.049). All dogs that engrafted developed multiorgan GVHD. To facilitate in vivo tracking, 8 dogs received CTLs transduced with a retroviral vector encoding green fluorescent protein (GFP) and neomycin phosphotransferase (neo). Recipients that engrafted had sharp increases in the numbers of circulating GFP(+) CTLs on days +5 to +6 after transplantation. GFP(+) CTLs isolated from blood were capable of recipient-specific lysis. At necropsy, up to 7.1% of CD3(+) cells in tissues were GFP(+) and polymerase chain reaction in situ hybridization for neo showed infiltration of transduced CTLs in GVHD-affected organs. These results show that ex vivo expanded, transduced T cells maintained in vivo function and enhanced marrow engraftment.

Animals↗
PubMed2001

Dependence of thermal mismatch broadening on column diameter in high-speed liquid chromatography at elevated temperatures.

In this paper, we compare a narrow-bore column (2.1-mm i.d.) to a conventional-bore column (4.6 mm i.d.) at elevated temperatures under conditions where thermal mismatch broadening is serious and show that narrow-bore columns offer significant advantages in terms of efficiency and peak shape at higher linear velocities. We conclude that the so-called thermal mismatch broadening effect is largely due to a radial retention factor gradient and not a radial viscosity gradient. The lower volumetric flow rates inherent with the use of narrower columns lead to lower linear velocity in the heater tubing and longer eluent residence times in the heater. Thus, with the same heater tubing at the same column linear velocity, narrow-bore columns give better thermal equilibration between the eluent and the column compared to wider bore columns. This means that high-temperature, ultrafast liquid chromatography no longer requires excessively long preheater tubing to thermally equilibrate the eluent to the column temperature. Consequently, the use of narrow-bore columns at high-temperature improves analysis speed and efficiency over wider bore columns. We also discuss the advantages of using liquid heat-transfer media as compared to air as the heat-transfer media. We show that an air bath ought not be used to heat the mobile phase because at high temperature (>80 degrees C) and high column linear velocity (> 1.5 cm/s) the length of tubing needed to heat the mobile phase to column temperature is prohibitively long. Using accurate, empirical heat-transfer correlations, we estimated the length of tubing needed to heat the eluent as a function of the column linear velocity for both air and liquid heat-transfer media.

Chromatography, Liquid↗
PubMed2001

Multiple alignment of complete sequences (MACS) in the post-genomic era.

Multiple alignment, since its introduction in the early seventies, has become a cornerstone of modern molecular biology. It has traditionally been used to deduce structure / function by homology, to detect conserved motifs and in phylogenetic studies. There has recently been some renewed interest in the development of multiple alignment techniques, with current opinion moving away from a single all-encompassing algorithm to iterative and / or co-operative strategies. The exploitation of multiple alignments in genome annotation projects represents a qualitative leap in the functional analysis process, opening the way to the study of the co-evolution of validated sets of proteins and to reliable phylogenomic analysis. However, the alignment of the highly complex proteins detected by today's advanced database search methods is a daunting task. In addition, with the explosion of the sequence databases and with the establishment of numerous specialized biological databases, multiple alignment programs must evolve if they are to successfully rise to the new challenges of the post-genomic era. The way forward is clearly an integrated system bringing together sequence data, knowledge-based systems and prediction methods with their inherent unreliability. The incorporation of such heterogeneous, often non-consistent, data will require major changes to the fundamental alignment algorithms used to date. Such an integrated multiple alignment system will provide an ideal workbench for the validation, propagation and presentation of this information in a format that is concise, clear and intuitive.

Amino Acid Sequence↗
PubMed2001

Unconventional superconductivity in CeIrIn5 and CeCoIn5: specific heat and thermal conductivity studies.

Low temperature specific heat and thermal conductivity measurements on the ambient pressure heavy fermion superconductors CeIrIn5 and CeCoIn5 reveal power law temperature dependences of these quantities below T(c). The low temperature specific heat in both CeIrIn5 and CeCoIn5 includes T2 terms, consistent with the presence of nodes in the superconducting energy gap. The thermal conductivity data present a T-linear term consistent with the universal limit (CeIrIn5), and a low temperature T3 variation in the clean limit (CeCoIn5), also in accord with prediction for an unconventional superconductor with lines of nodes.

Journal Article↗
PubMed2001

BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.

BAliBASE is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The database contains high quality, manually constructed multiple sequence alignments together with detailed annotations. The alignments are all based on three-dimensional structural superpositions, with the exception of the transmembrane sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Here we describe version 2.0 of the database, which incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. BAliBASE can be viewed at the web site http://www-igbmc.u-strasbg. fr/BioInfo/BAliBASE2/index.html or can be downloaded from ftp://ftp-igbmc.u-strasbg.fr/pub/BAliBASE2 /.

Algorithms↗
PubMed2001

Evidence for local outbreeding depression in the Mediterranean island endemic Anchusa crispa Viv. (Boraginaceae).

In this study we examined the relative effects of inbreeding and outbreeding on offspring fitness over two generations in Anchusa crispa Viv., a rare species which on Corsica (France) occurs in small populations composed of patches of few individuals. Self- and outcross-pollinations were carried out in a single population and F(1) progeny grown to flowering. Plants grown from selfing and outcrossing were then selfed or outcrossed to produce F(2) individuals in four combinations of pollination treatments over two generations, i.e. self + self, self + outcross, outcross + self and outcross + outcross. In the F(1) generation, selfed progeny had a significantly greater number of cymes per plant than outcrossed progeny (P=0.006). Plants from two generations of selfing had fewer seeds per fruit (P=0.06) but a significantly greater survival rate (P < 0.001) and a greater number of cymes (P=0.06) than those from two generations of outcrossing. Selfed F(2) from outcrossed F(1) had a significantly greater number of cymes (P < 0.01) than outcrossed F(2) from outcrossed F(1). In the comparison between selfed and outcrossed F(2) from selfed F(1) the former had a significantly greater survival rate (P < 0.001), but the latter significantly more flowers per cyme (P < 0.05). Together, these results indicate that outbreeding depression may occur on a very local scale within populations of this rare endemic species, with important implications for the conservation of rare plants.

Boraginaceae↗
PubMed2001

Opportunities for public health genetics trainees: results of an employer/workplace survey.

OBJECTIVE: To conduct the first employer/workplace survey identifying employment opportunities for graduates of programs with training in public health genetics in the USA, and to determine whether employment opportunities will increase in coming years. METHODS: Six public health genetics training competencies were developed. A survey about workplace and employment opportunities was then conducted with mailings to (1) departments in schools of public health and departments of preventive medicine, (2) local and regional public health officials, (3) insurance companies and health management organizations (HMOs), and (4) biotechnology and pharmaceutical companies. RESULTS: A total of 196 surveys were returned among 1,464 that were mailed. Response rates varied from 5.8 to 46.5% among the target groups. The percent of responding organizations currently employing individuals with skills in genetics ranged from 20 to 62%. The percent currently employing individuals with skills in public health ranged from 39 to 96%. Training opportunities such as internships or practicum experiences are reported for one-third of respondents. For all of the competencies, approximately half of survey respondents who rated the competency important or very important already employ individuals with public health genetics skills. Similarly, at least a quarter of survey respondents who rated the competency important or very important plan to hire individuals with that skill in the next 5 years. Overall, approximately 40% of those surveyed are planning to hire individuals with competencies in public health genetics in the next 5 years. CONCLUSION: Employment opportunities already exist and new positions are becoming available in schools of public health and departments of preventive medicine, departments of public health, insurance companies and HMOs for professionals with public health genetics training. Based on our survey findings, skills and training in public health genetics are important in the workplace.

Journal Article↗
PubMed2000

DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.

DbClustal addresses the important problem of the automatic multiple alignment of the top scoring full-length sequences detected by a database homology search. By combining the advantages of both local and global alignment algorithms into a single system, DbClustal is able to provide accurate global alignments of highly divergent, complex sequence sets. Local alignment information is incorporated into a ClustalW global alignment in the form of a list of anchor points between pairs of sequences. The method is demonstrated using anchors supplied by the Blast post-processing program, Ballast. The rapidity and reliability of DbClustal have been demonstrated using the recently annotated Pyrococcus abyssi proteome where the number of alignments with totally misaligned sequences was reduced from 20% to <2%. A web site has been implemented proposing BlastP database searches with automatic alignment of the top hits by DbClustal.

Algorithms↗
PubMed2000

Adoptive immunotherapy in canine mixed chimeras after nonmyeloablative hematopoietic cell transplantation.

Development of nontoxic and nonmyeloablative regimens for allogeneic hematopoietic stem-cell transplantation will decrease transplantation-related mortality caused by regimen-related toxic effects. In pursuit of this goal, a dog model of stable mixed hematopoietic chimerism was established in which leukocyte-antigen-identical litter mates are given sublethal total-body irradiation (2 Gy) before stem-cell transplantation and immunosuppression with mycophenolate mofetil and cyclosporine afterward. In the current study, we examined whether donor lymphocyte infusion (DLI) could be used as adoptive immunotherapy to convert mixed to complete donor chimerism. First, 8 mixed chimeras were given unmodified DLI between day 36 and day 414 after stem-cell transplantation. After a 10- to 47-week follow-up period, there were no significant changes in the percentage of donor engraftment. Next, we immunized the donor to the minor histocompatibility antigens (mHA) of the recipient by means of repeated skin grafting. Lymphocytes from the mHA-sensitized donor were infused between day 201 and day 651 after transplantation. All 8 recipients of mHA-sensitized DLI had conversion to greater than 98% donor chimerism within 2 to 12 weeks of the infusion. Complications from mHA-sensitized DLI included graft-versus-host disease in 2 dogs and marrow aplasia in 1. These results showed that the low-dose transplant regimen establishes immune tolerance, and mHA-sensitized DLI is required to break tolerance, thereby converting mixed to complete donor chimerism. We propose that mixed chimerism established after nonmyeloablative allogeneic stem-cell transplantation provides a platform for adoptive immunotherapy that has clinical potential in the treatment of patients with malignant diseases.

Animals↗
PubMed2000

Frequency of BRCA1/BRCA2 mutations in a population-based sample of young breast carcinoma cases.

BACKGROUND: There is a clear and growing need for data regarding BRCA1 and BRCA2 mutation frequencies among breast carcinoma cases not specifically ascertained on the basis of extreme family history profiles. Toward this end, the authors previously reported results with regard to BRCA1 in breast carcinoma patients drawn from a population-based study. In the current study the authors present new findings concerning BRCA2 mutation frequency in this same population, as well as summary data regarding the combined contribution of these two genes. METHODS: Subjects were drawn from two population-based, case-control studies of breast carcinoma in young women conducted in western Washington State and focused on 1) women diagnosed with breast carcinoma before age 35 years (n = 203); and 2) women with a first-degree family history of breast carcinoma who were diagnosed before age 45 years (n = 225). Similarities and differences between BRCA2 carriers and BRCA1 carriers were analyzed in terms of age at diagnosis, family history status, and disease features. RESULTS: Of cases diagnosed before age 35 years, all of whom were unselected for family history, 9.4% carried germline mutations (3.4% for BRCA2 and 5.9% for BRCA1). Of cases diagnosed before age 45 years who had a first-degree family history of breast carcinoma, 12.0% carried germline mutations (4.9% for BRCA2 and 7.1% for BRCA1). Increased frequencies of mutations were observed in cases with a personal or family history of early age at diagnosis and in those with four or more family members affected with breast carcinoma. BRCA2 mutations were less common than BRCA1 mutations in families with any history of ovarian carcinoma. CONCLUSIONS: Overall, given current constraints on health care resources, these data suggest that screening for germline mutations in these breast carcinoma susceptibility genes may have the greatest impact on overall health care if it is prioritized toward high and moderate risk populations.

Adult↗
PubMed2000

Evolution and maintenance of stigma-height dimorphism in Narcissus. I. Floral variation and style-morph ratios.

An unusual stylar dimorphism occurs in Narcissus, a plant genus of insect-pollinated Mediterranean geophytes. To determine the characteristics of the sexual polymorphism, we investigated floral variation in 46 populations of N. assoanus (section Jonquillae) and 21 populations of N. dubius (section Tazettae) in SW France. Flowers possess two stamen levels in each morph that occupy slightly different positions within the floral tube. In long-styled plants (L-morph), the stigma is located within or slightly above the upper-level stamens, whereas in short-styled plants (S-morph) the stigma is placed well below the lower-level stamens. The stigma-height dimorphism is distinct from heterostyly because the reciprocity of stigma and anther positions in the two style morphs is only weakly developed and there are no differences between the style morphs in pollen size or production. In both species, mean stigma-anther separation is much greater in the S-morph than the L-morph. In N. assoanus, population style-morph ratios vary from isoplethy (1L:1S) to L-biased, whereas in N. dubius they are usually strongly L-biased or occasionally contain only the L-morph. Populations fixed for the S-morph, or with S-biased morph ratios, were not observed. In N. assoanus, style-morph ratios were associated with population size: large continuous populations always exhibited 1:1 morph ratios, whereas smaller, fragmented populations were often L-biased. This pattern was not evident in N. dubius. We argue that biased style-morph ratios largely result from morph-specific differences in assortative mating.

Biological Evolution↗
PubMed2000

Evolution and maintenance of stigma-height dimorphism in Narcissus. II. Fitness comparisons between style morphs.

Populations of the insect-pollinated geophytes Narcissus assoanus and N. dubius (Amaryllidaceae) are commonly dimorphic for stigma height. An extensive survey of populations of the two species in SW France revealed a wide range of style-morph frequencies, particularly populations with significantly more long-styled than short-styled plants. Here we employ experimental and theoretical approaches to investigate potential selective mechanisms governing the variation in style-morph frequencies. Controlled pollination of both species demonstrated that N. assoanus is moderately self-sterile whereas N. dubius is highly self-compatible. Both intra- and intermorph crosses of N. assoanus were equally fertile, indicating that the species does not exhibit heteromorphic incompatibility. Estimates of female fertility (fruit- and seed-set) and multilocus estimates of outcrossing using allozyme markers provided no evidence of morph-specific differences in maternal components of reproductive success in natural populations of the two species. This result suggested that differences between the morphs in male fertility may be largely responsible for the observed morph-ratio variation. To investigate this hypothesis we developed a mating model that incorporates the genetics of stigma-height dimorphism and contrasting rates of assortative and disassortative mating in the style morphs. Simulation results demonstrated that stigma-height dimorphism will always be maintained when levels of disassortative mating are greater than assortative mating, and that the observed L-biased populations in Narcissus spp. probably result from greater levels of assortative mating in this morph in comparison with the S-morph.

Biological Evolution↗
PubMed2000

Ballast: blast post-processing based on locally conserved segments.

MOTIVATION: Blast programs are very efficient in finding relatively strong similarities but some very distantly related sequences are given a very high Expect value and are ranked very low in Blast results. We have developed Ballast, a program to predict local maximum segments (LMSs-i.e. sequence segments conserved relatively to their flanking regions) from a single Blast database search and to highlight these divergent homologues. The TBlastN database searches can also be processed with the help of information from a joint BlastP search. RESULTS: We have applied the Ballast algorithm to BlastP searches performed with sequences belonging to well described dispersed families (aminoacyl-tRNA synthetases; helicases) against the SwissProt 38 database. We show that Ballast is able to build an appropriate conservation profile and that LMSs are predicted that are consistent with the signatures and motifs described in the literature. Furthermore, by comparing the Blast, PsiBlast and Ballast results obtained on a well defined database of structurally related sequences, we show that the LMSs provide a scoring scheme that can concentrate on top ranking distant homologues better than Blast. Using the graphical user interface available on the Web, specific LMSs may be selected to detect divergent homologues sharing the corresponding properties with the query sequence without requiring any additional database search.

Algorithms↗
PubMed2000

Exploring the genetic basis and proximate causes of female fertility advantage in gynodioecious Thymus vulgaris.

In many gynodioecous species, females produce more viable seeds than hermaphrodites. Knowledge of the relative contribution of inbreeding depression in hermaphrodites and maternal sex effects to the female fertility advantage and the genetic basis of variation in female fertility advantage is central to our understanding of the evolution of gender specialization. In this study we examine the relative contribution of inbreeding and maternal sex to the female fertility advantage in gynodioecious Thymus vulgaris and quantify whether there is genetically based variation in female fertility advantage for plants from four populations. Following controlled self and outcross (sib, within-population, and between-population) pollination, females had a more than twofold fertility advantage (based on the number of germinating seeds per fruit), regardless of the population of origin and the type of pollination. Inbreeding depression on viable seed production by hermaphrodites occurred in two populations, where inbreeding had been previously detected. Biparental inbreeding depression on viable seed production occurred in three of four populations for females, but in only one population for hermaphrodites. Whereas the maternal sex effect may consistently enhance female fertility advantage, inbreeding effects may be limited to particular population contexts where inbreeding may occur. A significant family x maternal sex interaction effect on viable seed production was observed, illustrating that the extent of female fertility advantage varies significantly among families. This result is due to greater variation in hermaphrodite (relative to female) seed fertility between families. Despite this genetic variation in female fertility advantage and the highly female biased sex ratios in populations of T. vulgaris, gynodioecy is a stable polymorphism, suggesting that strong genetic and/or ecological constraints influence the stability of this polymorphism.

Analysis of Variance↗
PubMed2000

The effects of population size limitation on fecundity in mosaic populations of the clonal macrophyte Scirpus maritimus (Cyperaceae).

The clonal macrophyte Scirpus maritimus (Cyperaceae) propagates locally by rhizomes and reproduces sexually by achenes. The purpose of this paper was to examine whether in size-limited habitats in patchy and discrete marshes in two Mediterranean wetlands in southern France natural populations may suffer from a reduced maternal fecundity due to a deficit in outcross pollen. We first verified that S. maritimus suffers from a reduced fecundity when self-pollinated. At a site in the Camargue, mean fecundity (mean number of achenes per centimetre of spikelet) measured in 1995 and 1996 in seven and nine populations, respectively (surface area from 50 to 4500 m) increased significantly with population surface area in 1995 but not in 1996. In the second wetland at Roquehaute, which is composed of small ponds, fecundity was very low in all 12 local populations studied in 1996 (1.1 achenes per spikelet, SD = 1.2) and was not correlated with the population surface area (from 10 to 400 m). We performed a pollen supplementation experiment in five local populations at Roquehaute to determine whether this low fecundity may be due to a pollen limitation. A significant increase in fecundity after among-pond pollinations compared to within-pond pollinations indicated that local populations suffer from a deficit in outcross pollen, since each pond appears to contain one or a few number of clones (or incompatibility types). In S. maritimus, clonal spread may have a cost in terms of reduced fecundity in small habitats because each habitat is colonized by very few clones.

Journal Article↗
PubMed2000

Apophyseal fracture of the greater trochanter.

Apophyseal fractures about the pelvis and proximal femur are well-described; however, these injuries rarely involve the greater trochanter. We report the case of a 15-year-old boy of large build who appeared to have all signs and symptoms of a left slipped capital femoral epiphysis. No specific inciting event had occurred before the hip pain. Radiographs and bone scan of the capital femoral epiphysis appeared normal, and follow-up radiographs confirmed an apophyseal fracture of the greater trochanter. This case represented a rare occurrence, and its interesting manifestation was similar to that of a slipped capital femoral epiphysis.

Adolescent↗
PubMed1999

3-O-Desacyl monophosphoryl lipid A derivatives: synthesis and immunostimulant activities.

The synthesis of a series of novel analogues of lipid A, the active principle of lipopolysaccharide, is reported. In these compounds, the 1-O-phosphono and (R)-3-hydroxytetradecanoyl moieties of native Salmonella minnesota R595 lipid A have been replaced with hydrogen and the length of the normal fatty acyl residues has been systematically varied. Normal fatty acid chain length in the 3-O-desacyl monophosphoryl lipid A (MLA) series is shown to be a critical determinant of iNOS gene expression in activated mouse macrophages and the induction of proinflammatory cytokines in human peripheral monocytes. Examination of pyrogenicity in rabbits and lethal toxicity in D-galactosamine-treated mice shows that toxic effects in the MLA series can be ameliorated by modifying fatty acid chain length. When used as an adjuvant for tetanus toxoid vaccines, certain MLA derivatives enhance the production of tetanus toxoid-specific antibodies in mice.

Adjuvants, Immunologic↗