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L Yu

Publications and source records attributed to L Yu.

At least 199 records · Page 11Linked to original sources
PubMed2000

Structure characterization of human RalGDS gene, and the identification of its novel variant.

RalGDS is a guanine nucleotide dissociation stimulator for Ral, which is a member of the Ras GTPase superfamily that regulates cellular proliferation, differentiation and transformation by mediating multiple signal transduction pathways. RalGDS can specifically promote the conversion from an inactive GDP-bound state to an active GTP-bound state for Ral. The cDNA of human RalGDS has been cloned recently. In this paper, by comparison between the gene's genomic and cDNA seqence, we determined the structure of the gene, which showed that the reported human RalGDS transcribed from 18 exons. Furthermore, a novel variant of RalGDS that codes for a protein with a different N-terminus was cloned and identified. Northern hybridization revealed that the novel transcript was of 6.0 kb in length while the transcript previously reported is of 4.0 kb. Both transcripts were ubiquitously expressed in human adult tissues examined, albeit with different amounts. In addition, this novel transcript was proved to be caused by employment of a new exon, designated as exon 1a, instead of the one, designated as exon 1b, in the reported cDNA. Thus, the RalGDS gene consists of at least 19 exons and spanned a 44 kb region. The length between exon 1a and exon 2 was 33 kb, while the length between exon 1b and exon 2 was 8.8 kb.

Amino Acid Sequence↗
PubMed2000

Aberrant CpG-island methylation has non-random and tumour-type-specific patterns.

CpG islands frequently contain gene promoters or exons and are usually unmethylated in normal cells. Methylation of CpG islands is associated with delayed replication, condensed chromatin and inhibition of transcription initiation. The investigation of aberrant CpG-island methylation in human cancer has primarily taken a candidate gene approach, and has focused on less than 15 of the estimated 45,000 CpG islands in the genome. Here we report a global analysis of the methylation status of 1,184 unselected CpG islands in each of 98 primary human tumours using restriction landmark genomic scanning (RLGS). We estimate that an average of 600 CpG islands (range of 0 to 4,500) of the 45,000 in the genome were aberrantly methylated in the tumours, including early stage tumours. We identified patterns of CpG-island methylation that were shared within each tumour type, together with patterns and targets that displayed distinct tumour-type specificity. The expression of many of these genes was reactivated by experimental demethylation in cultured tumour cells. Thus, the methylation of particular subsets of CpG islands may have consequences for specific tumour types.

Adenocarcinoma↗
PubMed2000

Up-regulation of base excision repair activity for 8-hydroxy-2'-deoxyguanosine in the mouse brain after forebrain ischemia-reperfusion.

The repair enzyme 8-oxoguanine glycosylase/ apyrimidinic/apurinic lyase (OGG) removes 8-hydroxy-2'deoxyguanosine (oh8dG) in human cells. Our goal was to examine oh8dG-removing activity in the cell nuclei of male C57BL/6 mouse brains treated with either forebrain ischemia-reperfusion (FblR) or sham operations. We found that the OGG activity in nuclear extracts, under the condition in which other nucleases did not destroy the oligodeoxynucleotide duplex, excised oh8dG with the greatest efficiency on the oligodeoxynucleotide duplex containing oh8dG/dC and with less efficiency on the heteroduplex containing oh8dG/dT, oh8dG/dG, or oh8dG/dA. This specificity was the same as for the recombinant type 1 OGG (OGG1) of humans. We observed that the OGG1 peptide and its activity in the mouse brain were significantly increased after 90 min of ischemia and 20-30 min of reperfusion. The increase in the protein level and in the activity of brain OGG1 correlated positively with the elevation of FblR-induced DNA lesions in an indicator gene (the c-fos gene) of the brain. The data suggest a possibility that the OGG1 protein may excise oh8dG in the mouse brain and that the activity of OGG1 may have a functional role in reducing oxidative gene damage in the brain after FblR.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2000

Thirty-plus functional families from a single motif.

It is now possible to identify over 30 functional subfamilies among the WD-repeat-containing proteins found in the completed genomes. The majority of these subfamilies have at least one member for which experimental data allow assignment to a cellular pathway or process. Half of the 63 WD-repeat-containing proteins in Saccharomyces cerevisiae, half of the 70 in Caenorhabditis elegans, and a third of the 100 plus predicted in Drosophila can be assigned to 23 of these functional subfamilies. Perhaps indicative of the future, 33 WD-repeat-containing proteins from the partial genome of Arabidopsis thaliana can now be assigned to 18 of these subfamilies. These assignments have been made possible by combining traditional sequence similarity with an implied common beta propeller structural context to obtain measures of protein-protein surface similarity. The beta propeller structural context is represented in the form of a Hidden Markov Model. The procedure is completely automated.

Algorithms↗
PubMed2000

Subunit-specific action of an anticonvulsant thiobutyrolactone on recombinant glycine receptors involves a residue in the M2 membrane-spanning region.

The anticonvulsant alpha-ethyl, alpha-methyl-gamma-thiobutyrolactone (alphaEMTBL) potentiates the response to a submaximal concentration of glycine produced by receptors composed of human glycine alpha1-subunits but reduces the response of receptors composed of rat glycine alpha3-subunits. Both the potentiating and blocking actions of alphaEMTBL are reduced by higher concentrations of glycine. The subunit specificity of alphaEMTBL block is conferred by a residue in the second membrane-spanning region (M2), which is alanine in the alpha3-subunit (A254) and glycine in the alpha1-subunit. The mutation A254G in the alpha3-subunit removes blocking by alphaEMTBL and reveals potentiation. Picrotin, a picrotoxinin analog, blocks responses of receptors composed of either alpha1 or alpha3-subunits. Blocking of alpha3 receptors by picrotin is reduced in the presence of alphaEMTBL, indicating that the mechanisms interact at some point, but the mutation alpha3 A254G does not remove block by picrotin. However, mutation of a nearby residue alpha3 T258F does remove block by picrotin, picrotoxinin and alphaEMTBL. These observations suggest that alphaEMTBL and picrotin act on glycine alpha3 receptors to produce block by an allosteric mechanism that involves overlapping sets of residues in the M2 region. Coexpression of the alpha3-subunit with the beta-subunit of the glycine receptor also removes block by alphaEMTBL and reveals potentiation, suggesting that receptors containing either alpha3 or alpha1 glycine receptor subunits are potentiated in the adult brain.

4-Butyrolactone↗
PubMed2000

Selected chitinase genes in cultured and uncultured marine bacteria in the alpha- and gamma-subclasses of the proteobacteria.

PCR primers were patterned after chitinase genes in four gamma-proteobacteria in the families Alteromonadaceae and Enterobacteriaceae (group I chitinases) and used to explore the occurrence and diversity of these chitinase genes in cultured and uncultured marine bacteria. The PCR results from 104 bacterial strains indicated that this type of chitinase gene occurs in two major groups of marine bacteria, alpha- and gamma-proteobacteria, but not the Cytophaga-Flavobacter group. Group I chitinase genes also occur in some viruses infecting arthropods. Phylogenetic analysis indicated that similar group I chitinase genes occur in taxonomically related bacteria. However, the overall phylogeny of chitinase genes did not correspond to the phylogeny of 16S rRNA genes, possibly due to lateral transfer of chitinase genes between groups of bacteria, but other mechanisms, such as gene duplication, cannot be ruled out. Clone libraries of chitinase gene fragments amplified from coastal Pacific Ocean and estuarine Delaware Bay bacterioplankton revealed similarities and differences between cultured and uncultured bacteria. We had hypothesized that cultured and uncultured chitin-degrading bacteria would be very different, but in fact, clones having nucleotide sequences identical to those of chitinase genes of cultured alpha-proteobacteria dominated both libraries. The other clones were similar but not identical to genes in cultured gamma-proteobacteria, including vibrios and alteromonads. Our results suggest that a closer examination of chitin degradation by alpha-proteobacteria will lead to a better understanding of chitin degradation in the ocean.

Alphaproteobacteria↗
PubMed2000

Assembly of double-shelled, virus-like particles in transgenic rice plants expressing two major structural proteins of rice dwarf virus.

Rice dwarf virus (RDV) is a double-shelled particle that contains a major capsid protein (P8), a major core protein (P3), several minor core proteins, and viral genomic double-stranded RNA. Coexpression of P8 and P3 in transgenic rice plants resulted in formation of double-shelled, virus-like particles (VLPs) similar to the authentic RDV particles. The VLPs were not detected in transgenic rice plant cells expressing P8 alone. This in vivo result suggests that P8 interacted with P3 and that these two proteins provide the structural integrity required for the formation of VLPs in rice cells independently of other structural proteins, nonstructural proteins, or viral genomic double-stranded RNAs.

Capsid↗
PubMed2000

Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling.

Transcriptional activators are believed to work in part by recruiting general transcription factors, such as TATA-binding protein (TBP) and the RNA polymerase II holoenzyme. Activation domains also contribute to remodeling of chromatin in vivo. To determine whether these two activities represent distinct functions of activation domains, we have examined transcriptional activation and chromatin remodeling accompanying artificial recruitment of TBP in yeast (Saccharomyces cerevisiae). We measured transcription of reporter genes with defined chromatin structure by artificial recruitment of TBP and found that a reporter gene whose TATA element was relatively accessible could be activated by artificially recruited TBP, whereas two promoters, GAL10 and CHA1, that have accessible activator binding sites, but nucleosomal TATA elements, could not. A third reporter gene containing the HIS4 promoter could be activated by GAL4-TBP only when a RAP1 binding site was present, although RAP1 alone could not activate the reporter, suggesting that RAP1 was needed to open the chromatin structure to allow activation. Consistent with this interpretation, artificially recruited TBP was unable to perturb nucleosome positioning via a nucleosomal binding site, in contrast to a true activator such as GAL4, or to perturb the TATA-containing nucleosome at the CHA1 promoter. Finally, we show that activation of the GAL10 promoter by GAL4, which requires chromatin remodeling, can occur even in swi gcn5 yeast, implying that remodeling pathways independent of GCN5, the SWI-SNF complex, and TFIID can operate during transcriptional activation in vivo.

Chromatin↗
PubMed2000

Pain genes?: natural variation and transgenic mutants.

Like many other complex biological phenomena, pain is starting to be studied at the level of the gene. Advances in molecular biological technology have allowed the cloning, mapping, and sequencing of genes, and also the ability to disrupt their function entirely (i.e. via transgenic knockouts). With these new tools at hand, pain researchers have begun in earnest the task of defining (a) which of the 70,000-150,000 mammalian genes are involved in the mediation of pain, and (b) which of the pain-relevant genes are polymorphic, contributing to both natural variation in responses and pathology. Although there are only a few known examples in which single gene mutations in humans are associated with pain conditions (e.g. an inherited form of migraine and congenital insensitivity to pain), it is likely that others will be identified. Concurrently, a variety of genes have been implicated in both the transmission and control of "pain" messages in animals. The present review summarizes current progress to these ends, focusing on both transgenic (gene-->behavior) and classical genetic (behavior-->gene) approaches in both humans and laboratory mice.

Analgesia↗
PubMed2000

Breath-hold three-dimensional contrast-enhanced coronary MR angiography: motion-matched k-space sampling for reducing cardiac motion effects.

A view order that matches k-space sampling to cardiac motion within the acquisition window was developed for breath-hold three-dimensional contrast material-enhanced coronary magnetic resonance angiography. In vivo experiments in seven volunteers demonstrated that blurring was substantially reduced with this motion-matched view order as compared with the standard centric view order. Coronary arteries were well delineated.

Adult↗
PubMed2000

Transient antiislet autoantibodies: infrequent occurrence and lack of association with "genetic" risk factors.

We hypothesized that genetic determinants of expression of persistent antiislet autoantibodies would similarly influence the expression of transient autoantibodies. To test this hypothesis, we prospectively evaluated sera from 478 relatives (SOC: sibling-offspring cohort) of patients with type 1 diabetes as well as 793 newborns from the general population (NEC: newborn nonrelative cohort) selected for expression of specific human leukocyte antigen haplotypes. Eight relatives of 478 (1.7% of SOC) expressed a transient autoantibody, and none had the high risk genotype DR3/4(DQ2/8). In contrast, 28 relatives (5.9%) had persistent antiislet autoantibodies, and 14 (50%) were DR3/4(DQ2/8) heterozygotes. Thirteen children of 793 (1.6% of NEC) expressed a transient autoantibody, and none had the high risk genotype DR3/4(DQ2/8). Seven of the NEC (0.9%) had persistent antiislet autoantibodies, and 4 (57.1%) were DR3/4(DQ2/8) heterozygous. Expression of persistent autoantibodies was strongly related to human leukocyte antigen status and family history of type 1 diabetes. In contrast, the expression of transient antiislet autoantibodies did not differ by family history of diabetes, and none of the DR3/4(DQ2/8) relatives and DR3/4(DQ2/8) newborns expressed transient autoantibodies. Our results indicate that children can express transient antiislet autoantibodies, but such transient autoantibodies are relatively infrequent and are not correlated with known genetic risk factors for type 1 diabetes.

Aging↗
PubMed2000

Renal protective effects of blocking the intrarenal renin-angiotensin system: angiotensin II type I receptor antagonist compared with angiotensin-converting enzyme inhibitor.

The present study compared renoprotective effects of angiotensin II type I receptor antagonist (AT1RA) with angiotensin converting enzyme inhibitor (ACEI), and their influence on the renin-angiotensin-system (RAS). Experimental nephrotic syndrome was induced in SD rats by repeated peritoneal injections of puromycin. Twenty-eight rats were randomly divided into four groups: normal control, nephrotic control, ACEI-treated, and AT1RA-treated groups. Serum, urine, and renal tissue were collected for study at the end of 12 weeks. Compared with those of the nephrotic control group, urinary protein was less and renal function was better in both treated groups. The glomerular and interstitial damage indexes of both ACEI- and AT1RA-treated rats were lower than those of nephrotic control rats, with no significant difference observed between the two treated groups. Local renal ACE activity and angiotensin II concentration were elevated in nephrotic rats (p< 0.01). However, there is no significant difference in circulating RAS, renal tissue renin, and aldosterone between the normal control and nephrotic control rats. As expected, enalapril inhibited the local renal ACE activity and significantly decreased angiotensin II (p< 0.01). Intrarenal ACE activity and angiotensin concentration returned to normal levels after treatment with irbesartan (p< 0.01). In conclusion, AT1RA and ACEI have comparable renal protective effects, and these protective effects were associated with the inhibition of intrarenal ANG II.

Angiotensin Receptor Antagonists↗
PubMed2000

Cloning and characterization of CIS 1b (cytokine inducible SH2-containing protein 1b), an alternative splicing form of CIS 1 gene.

JAK-STAT pathway is essential in relaying cytokine signals and plays a vital role in cellular responses such as proliferation, differentiation and immunity. Some members of a recently found cytokine-inducible SH2 protein (CIS, =SOCS or SSI) family have proved to have negative effects on modulating JAK-STAT signaling pathway. In the present study, a novel human cDNA (CIS1b) which proved to be a variant of CIS1 gene was isolated by screen human placenta lambda gt11 cDNA library and 5'-rapid amplification of cDNA ends (RACE). Furthermore, the gene structure of CIS1 was determined by comparing the cDNA sequences of CIS1 and CIS1b to the genomic sequence in human chromosome 3p21.3. The expression patterns of CIS1b as well as CIS1 were analysed by Northern blot.

Alternative Splicing↗
PubMed2000

Pathologic evaluation of sentinel lymph nodes in colorectal carcinoma.

BACKGROUND: The identification of lymph node metastases in colorectal resection specimens is necessary for accurate tumor staging. However, routine lymph node dissection by the pathologist yields only a subset of nodes removed surgically and may not include those nodes most directly in the path of lymphatic drainage from the tumor. Intraoperative mapping of such sentinel lymph nodes (SLNs) has been reported in cases of melanoma and breast cancer. We applied a similar method to cases of colorectal carcinoma, with emphasis on the pathology of the SLNs. METHODS: Eighty-three consecutive patients with colorectal carcinoma were evaluated after intraoperative injection of 1 to 2 mL of 1% isosulfan blue dye (Lymphazurin) into the peritumoral subserosa. Blue-stained lymph nodes were suture-tagged by the surgeon within minutes of the injection for identification by the pathologist, and a standard resection was performed. Designated SLNs were sectioned at 10 levels through the block; a cytokeratin immunostain (AE1) was also obtained. To evaluate the possibility that increased detection of metastases in the SLN might be solely due to increased histologic sampling, all initially negative non-SLNs in the first 25 cases were sectioned also at 10 levels. RESULTS: Sentinel lymph nodes were identified intraoperatively in 82 (99%) of 83 patients and accounted for 152 (11.9%) of 1275 lymph nodes recovered, with an average of 1.9 SLNs per patient. A total of 99 positive lymph nodes (38 positive SLNs and 61 positive non-SLNs) were identified in 34 node-positive patients. The SLNs were the only site of metastasis in 17 patients (50%), while 14 patients (41%) had both positive SLNs and non-SLNs. Three patients (9%) had positive non-SLNs with negative SLNs, representing skip metastases. In patients with positive SLNs, 91 (19%) of 474 total lymph nodes and 53 (12%) of 436 non-SLNs were positive for metastasis. In patients with negative SLNs, 8 (1%) of 801 total lymph nodes and 8 (1.2%) of 687 non-SLNs were positive for metastasis. Multilevel sections of 330 initially negative non-SLNs in the first 25 patients yielded only 2 additional positive nodes (0. 6%). All patients with positive SLNs were correctly staged by a combination of 4 representative levels through the SLN(s) together with a single cytokeratin immunostain. CONCLUSIONS: Intraoperative mapping of SLNs in colorectal carcinoma identifies lymph nodes likely to contain metastases. Focused pathologic evaluation of the 1 to 4 SLNs so identified can improve the accuracy of pathologic staging.

Adult↗