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Biomedical subjects

B R Jordan

Publications and source records attributed to B R Jordan.

At least 19 recordsLinked to original sources
PubMed1997

Molecular cloning, sequencing and expression of the mRNA encoding human Cdx1 and Cdx2 homeobox. Down-regulation of Cdx1 and Cdx2 mRNA expression during colorectal carcinogenesis.

Defining the molecular mechanisms involved in cancer formation and progression is still a major challenge in colorectal-cancer research. Our strategy was to characterize genes whose expression is altered during colorectal carcinogenesis. To this end, the phenotype of a colorectal tumour was previously established by partial sequencing of a large number of its transcripts and the genes of interest were selected by differential screening on high-density filters with mRNA of colorectal cancer and normal adjacent mucosa. Fifty-one clones were found over-expressed and 23 were underexpressed in the colorectal-cancer tissues of the 5 analyzed patients. Among the latter, clones 6G2 and 32D6 were found of particular interest, since they had significant homology with several homeodomain-containing genes. The highest degree of similarity was with the murine Cdx1 for 6G2, and with the murine Cdx2 and hamster Cdx3 for 32D6. Using a RT-PCR approach, complete sequence of both types of homeobox-containing cDNA was obtained. The amino-acid sequence of the human Cdx1 is 85% identical to the mouse protein, and human Cdx2 has 94% identity with the mouse Cdx2 and hamster Cdx3. Tissue-distribution analysis of Cdx1 and Cdx2 mRNA showed that both transcripts were specifically expressed in small intestine, in colon and rectum. Twelve tissue samples from colorectal adenocarcinomas and the corresponding normal mucosa were analyzed by Northern blot. Expression of the 2 types of mRNA was either reduced or absent in 10 of them. Several colon-cancer cell lines were also analyzed. Cdx2 mRNA was absent from LS174T cells and Cdx1 mRNA was absent in PF11, TC7 and SW480 cells; none was detected in HT29 cells. It was concluded that decrease in human Cdx1 and/or Cdx2 expression is associated with colorectal tumorigenesis.

Adenocarcinoma↗
PubMed1997

Differential mRNA expression in untreated and TNF-alpha elicited murine dendritic cells precursors.

We have compared the pattern of gene expression in long term cultured precursor dendritic cells (DC), either untreated (immature) or cultured for two days in the presence of recombinant murine (rm)-TNF alpha (mature). The hybridization signature of complex cDNA probes prepared from total RNA extracted from immature and mature DC were analyzed using a mouse thymic cDNA library, gridded on high density filters. For each clone spotted on the filters, we have measured using an imaging plate device the hybridization signals of the complex probe obtained from immature or mature DC. Comparative analysis of these values allowed us to identify differentially expressed gene products. Our goal is to identify a new set of genes induced or repressed during DC maturation elicited by rmTNF alpha treatment.

Animals↗
PubMed1997

Modulation of mRNA levels in the presence of thymocytes and genome mapping for a set of genes expressed in mouse thymic epithelial cells.

Modulation of gene expression in mouse thymic epithelium upon culture in the presence of thymocytes (coculture) was studied by comparison of hybridization signatures on a set of nearly 5000 mouse thymus cDNA clones. Forty-nine differentially expressed clones (usually down-regulated in coculture) were characterized by tag sequencing. Many of them corresponded to entities that had not been described previously in the mouse, and were further characterized by genome mapping. This set of genes appears to be involved in growth regulation and differentiation within the thymus.

Animals↗
PubMed1996

Multiplex messenger assay: simultaneous, quantitative measurement of expression of many genes in the context of T cell activation.

The hybridization signature approach, using colony filters and labeled complex probes, can provide high throughput measurement of gene activity. We describe here the implementation of this method to follow the expression levels of 47 genes in resting and activated T cells, as well as in epithelial cells. Using 4-fold spotting of colonies, imaging plate detection and various correction and normalization procedures, the technique is sensitive enough to quantify expression levels for sequences present at 0.005% abundance in the probe. Comparison with Northern blotting shows good consistency between the two methods. Upon activation of a T cell clone by an anti-CD3 antibody variations ranging from 2- to 20-fold are measured, some of which had not been reported previously. This 'multiplex messenger assay' method, performed using available commercial apparatus, can be used in many cases where simultaneous assessment of mRNA levels for many genes is of interest.

Animals↗
PubMed1996

From hybridization image to numerical values: a practical, high throughput quantification system for high density filter hybridizations.

Hybridization to sets of bacterial colonies or PCR products arrayed on high density filters is used in a number of experimental schemes. In many cases it is desirable to collect quantitative information ('hybridization signatures') rather than indications on 'positive' and 'negative' colonies. We present a practical system, based on an imaging plate analyser and a customized version of commercial software, that makes such quantification feasible, and define its performance in terms of reproducibility and linearity. The system is far superior to methods based on autoradiography and should be useful in many projects that involve the increasingly popular high density filter format.

Animals↗
PubMed1995

Differential gene expression in the murine thymus assayed by quantitative hybridization of arrayed cDNA clones.

High-throughput measurement of hybridization signatures obtained using complex probes prepared from poly(A)+ RNA and high-density cDNA colony filters is described. The performance of the system, elimination of artifacts, and verification of the validity of the data are discussed. cDNAs corresponding to sequences present at levels of approximately 0.01% in the complex probe can be detected. Good correlation is observed between expression profiles determined by this method and by Northern blotting. The method is applied to a preliminary investigation of differential expression in three cell types present in the murine thymus.

Animals↗
PubMed1994

Genome programmes: an opportunity for biology.

The development of human molecular genetics in the eighties led to the implementation of projects aimed at a systematic study of the human genetic make-up--the so-called "Genome Projects". These have so far been mainly concerned with genome mapping, both by family studies using polymorphic markers (genetic mapping) and by direct analysis of DNA with suitable fractionation and cloning methods (physical mapping). Major progress has been made in both fields recently. Sequencing per se has remained limited because of technical constraints, although systematic cDNA sequencing has caught on in a large way. National policies are quite diverse, with the USA, the UK, France and Japan being the major players; funding sources range from governments to foundations. Many of the results, methods and concepts obtained or implemented during genome studies can be of great use to "conventional" laboratories, and efficient interfacing between these two worlds is an increasingly important issue.

Base Sequence↗
PubMed1993

Cloning and sequence analysis of a flo/lfy homologue isolated from cauliflower (Brassica oleracea L. var. botrytis).

A cDNA library has been constructed from cauliflower curd in which floral development had been initiated. Two cDNAs (pBOFH3 and pBOFH8) have been isolated using the Antirrhinum flo gene as a heterologous probe. The two clones were sequenced and found to contain introns. Comparison of the deduced cDNA sequence of bofh with flo and the Arabidopsis homologue lfy reveals extensive homology. An mRNA transcript of 1.6 kb appears on northern RNA blots. This transcript can be detected, at low levels, before any obvious signs of floral differentiation, reflecting the role bofh plays in determining floral meristem identity.

Amino Acid Sequence↗
PubMed1991

Reduction in cab and psb A RNA transcripts in response to supplementary ultraviolet-B radiation.

The cab and psb A RNA transcript levels have been determined in Pisum sativum leaves exposed to supplementary ultraviolet-B radiation. The nuclear-encoded cab transcripts are reduced to low levels after only 4 h of UV-B treatment and are undetectable after 3 days exposure. In contrast, the chloroplast-encoded psb A transcript levels, although reduced, are present for at least 3 days. After short periods of UV-B exposure (4 h or 8 h), followed by recovery under control conditions, cab RNA transcript levels had not recovered after 1 day, but were re-established to ca. 60% of control levels after 2 more days. Increased irradiance during exposure to UV-B reduced the effect upon cab transcripts, although the decrease was still substantial. These results indicate rapid changes in the cellular regulation of gene expression in response to supplementary UV-B and suggest increased UV-B radiation may have profound consequences for future productivity of sensitive crop species.

Blotting, Northern↗
PubMed1991

Fragile X-linked mental retardation and the difficulties of reverse genetics.

Fragile X-linked mental retardation is an enigmatic inheritable syndrome in which severe mental retardation, a cytogenetically detectable fragile site at Xq27.3 (FraX) and a number of dysmorphic features are associated. Genetic analysis shows that the mode of inheritance is more complex than a straightforward X-linked recessive trait and probably involves a two-step process for which several models have been proposed. Early attempts at 'cloning the fragile site' provided several DNA segments lying in its general vicinity, and large scale DNA mapping methods were extensively applied in an effort to generate maps including this region. These efforts were complemented by more focussed methods such as microdissection; together these approaches have now provided a number of DNA segments within a 5 cM interval around FraX, and with the help of these new probes the site is indeed being cloned. Unravelling the nature of the sequence(s) responsible for the mental retardation syndrome will probably take some time, however.

Animals↗
PubMed1991

Laser microdissection of the fragile X region: identification of cosmid clones and of conserved sequences in this region.

Laser microdissection has been used to dissect material from the X-chromosome region involved in fragile-X-linked mental retardation. After dissection, single chromosome slices corresponding to this fragile site were subjected to DNA amplification using either a vector ligation method (to provide known anchor sequences) or primer oligonucleotides corresponding to the ubiquitous Alu sequences. Amplified material was then cloned or, alternately, used to screen a gridded cosmid library. Eight cosmid clones identified in this way were regionally mapped using a panel of hybrid cell lines and shown to originate from a narrow interval centered on the fragile X site. Two clones are included in the approximately 6-cM interval defined by probes RNI (DXS369, 5 cM proximal) and VK21 (DXS 296, 1-2 cM distal) and which includes the fragile site, and at least one clone contains sequences conserved across species suggestive of a gene. This method combines the focused approach of microdissection and the convenience of obtaining cosmid (rather than small-insert) clones; it may be useful for studies of other defined chromosomal regions.

Animals↗
PubMed1990

The gene encoding L1, a neural adhesion molecule of the immunoglobulin family, is located on the X chromosome in mouse and man.

The murine and human genes for the L1 neural adhesion molecule were shown to lie on conserved regions of the X chromosome to which genes responsible for several neuromuscular diseases have been mapped and which are adjacent to the fragile site (FRAXA) associated with mental retardation. By pulsed-field gel mapping we have demonstrated physical linkage between the L1 gene and other genes located in Xq28: L1 lies between the eye pigment RCP, GCP locus and the glucose-6-phosphate dehydrogenase (G6PD) gene. This location is compatible with the implication of the L1 molecule in one of the X-linked neuromuscular diseases mapped to this region.

Amino Acid Sequence↗
PubMed1989

Delineation of determinants on HLA-B7 and HLA-B27 that are necessary for cytolytic T cell recognition by using inter- and intra-domain recombinants.

We have used bulk culture HLA-B7 and HLA-B27 specific CTL lines derived from 11 donors, and a series of rHLA-B7/HLA-B27 genes transfected into and expressed on the surface of the murine cell P815, to determine the amino acid residues on these HLA class I molecules that are critical for allospecific CTL recognition. The results obtained indicate that for four of six HLA-B7-specific CTL lines the alpha-1 domain for CTL recognition. Furthermore, we found that residues 77 and/or 80 had a critical effect on recognition for all of the CTL lines tested. The region 97-156 in the alpha-2 domain was also important for some of these CTL lines. Furthermore, by using five bulk culture HLA-B27-specific CTL lines we were able to show that residues 77 and/or 80 and residue 152 are also essential for recognition of HLA-B27 by HLA-B27-specific CTL. The strong influence exerted by these residues is discussed in terms of the three-dimensional structure of class I molecules. Finally, a selection was regularly observed in the bulk cultures such that the CTL that were preferentially influenced by either the alpha-1 or the alpha-2 domain were lost after 4 to 7 wk of culture resulting in CTL cell lines which were extremely sensitive to sequence modifications of HLA-B7 or HLA-B27. The possible reasons for this selection, which we have previously observed with both anti-HLA-A2 and anti-HLA-A3 cell lines and is therefore not unique to HLA-B7 or HLA-B27, are discussed.

Cell Line↗
PubMed1989

Recognition of oligonucleotide-encoded T cell epitopes introduced into a gene unrelated to the original antigen.

We have previously demonstrated that H-2Kd-restricted CTL specific for HLA-CW3 or HLA-A24 can recognize synthetic peptides corresponding to residues 170-182 of the HLA molecules. Synthetic oligonucleotides encoding region 170-182 of CW3 or A24 were inserted into the influenza nucleoprotein (NP) gene. We demonstrate herein that P815 (H-2d) cells transfected with the NP-oligo recombinant genes are specifically lysed by HLA-specific Kd-restricted CTL clones. Our results imply that there must be a high degree of flexibility for the expression of T cell epitopes in different molecular contexts.

Animals↗