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S Chu

Publications and source records attributed to S Chu.

At least 19 recordsLinked to original sources
PubMed1998

Quantitation of TNP-470 and its metabolites in human plasma: sample handling, assay performance and stability.

A selective and sensitive assay for the determination of TNP-470 and two of its metabolites, AGM-1883 and M-II, in human plasma was developed. The assay involved liquid-liquid extraction followed by analysis using high-performance liquid chromatography-atmospheric pressure chemical ionization tandem mass spectrometry. Because TNP-470 is most stable in a pH of 4-5, an acidification procedure was utilized to prevent degradation of TNP-470 during sample collection which involved acidifying the whole blood sample collected with 5 mg of citric acid per ml of blood. Liquid-liquid extraction using an organic solvent mixture was chosen over solid-phase extraction to minimize the degradation of TNP-470 during solvent evaporation.

Acetamides↗
PubMed1998

Gametogenesis in yeast is regulated by a transcriptional cascade dependent on Ndt80.

Gametogenesis requires the successful coordination of two key processes, meiotic nuclear division and gamete morphogenesis. A central regulatory step in progression through gametogenesis occurs at the pachytene stage of meiotic prophase. We find that Ndt80 functions at pachytene of yeast gametogenesis (sporulation) to activate transcription of a set of genes required for both meiotic division (e.g., B-type cyclins) and gamete formation (e.g., SPS1). Ectopic synthesis of Ndt80 in vegetative cells induces transcription of these genes, and recombinant Ndt80 protein binds to a conserved sequence in their upstream region. Transcription of NDT80 itself is dependent on Ime1, which activates expression of early sporulation genes. Transcription of the Ndt80-regulated gene CLB1 is mediated by the checkpoint gene RAD17. Thus Ndt80 is a pivotal component of a transcriptional cascade programming yeast gametogenesis and may also be a target of meiotic checkpoint control.

Cyclin B↗
PubMed1998

Structural determinants of cortisol resistance in the guinea pig glucocorticoid receptor.

The guinea pig exhibits resistance to glucocorticoids in vivo which results from the guinea pig glucocorticoid receptor (GR) having a lower affinity for cortisol than the human GR. Cloning of the guinea pig GR has revealed that the amino acid sequence of the ligand-binding domain (LBD) differs from the human GR at 24 residues. The present study confirms that the decreased sensitivity and binding affinity of the guinea pig GR are conferred in vitro by the LBD. Further, the substitutions in the LBD do not confer altered relative steroid sensitivity or selectivity compared with the human GR. The altered sensitivity and binding of dexamethasone are confined to the first third of the LBD, which contains 5 nonconservative substitutions in a region that is otherwise highly conserved across several species of GR. These residues, either alone or in combination, were targeted for site-directed mutagenesis in both the human and guinea pig LBD. Trans-activation studies with these mutant GR failed to exclusively implicate or exclude any of the residues in the observed resistance. Rather, the changes, with 1 exception, caused a decrease in sensitivity, suggesting that critical intramolecular interactions involving at least 4 of these residues determine the correct conformation of this region. Recent molecular modeling of the GR LBD structure suggests that although the above region is not part of the core ligand-binding pocket, it is required to maintain the conformation of the binding pocket.

Amino Acid Sequence↗
PubMed1997

Alternative mRNA splice variants of the rat ClC-2 chloride channel gene are expressed in lung: genomic sequence and organization of ClC-2.

The ClC-2 epithelial cell chloride channel is a voltage-, tonicity- and pH-regulated member of the ClC super family. We have previously shown that rat lung ClC-2 (rClC-2) is down-regulated at birth, and molecular diversity is generated by alternative splicing [Murray et al. (1995) Am. J. Respir. Cell Mol. Biol. 12, 597-604; Murray et al. (1996) Am. J. Physiol. 271, L829-L837; Chu et al . (1996) Nucleic Acids Res. 24, 3453-3457]. To investigate other possible mRNA splice variations, we sequenced the entire rClC-2 gene and found that ClC-2Sa (formerly ClC-2S) results from the deletion of exon 20. The preceding intron 19 has an unusually high CT content and a rare AAG acceptor site. Because both features were also found in intron 13, we next tested the hypothesis that intron 13 would be involved in alternative splicing. As predicted, a second splice product, ClC-2Sb, was found by RT-PCR, but only in lung. When we compared the genomic maps of rClC-2 and human ClC-1 (hClC-1), striking similarities were found in each exon except for rClC-2 exon 20, which is absent in hClC-1. These observations suggest that ClC-1 and ClC-2 may have evolved by gene duplication, mutation and DNA rearrangement.

Alternative Splicing↗
PubMed1997

Identification of a splice variant of the rat estrogen receptor beta gene.

Recently a second estrogen receptor termed estrogen receptor beta (ERbeta) has been cloned and characterized, and shown to be expressed at the highest levels in ovarian granulosa cells and prostatic epithelium. In the course of amplifying a region of the ligand-binding domain of the rat ERbeta cDNA we identified a second, larger transcript which appears to arise through differential splicing. The second isoform has 54 nucleotides inserted after position 1372 encoding 18 additional amino acids. Both isoforms are expressed at similar relative abundance in a range of tissues.

Amino Acid Sequence↗
PubMed1997

Characterization of cationic liposome-mediated gene transfer in vivo by intravenous administration.

Physicochemical properties of the cationic liposomes, including structure of the cationic lipid-to-DNA ratio, liposome particle size, and inclusion of the helper lipids, were studied for their effect on the level, site, and duration time of gene expression in vivo by intravenous administration. Using a cytomegalovirus (CMV)-driven gene expression system containing either the luciferase or green fluorescence protein gene as a reporter and two cationic lipids [N-(2,3-dioleoyloxy)propyl-N,N,N-trimethylammonium chloride (DOTMA) and 1,2-dioleoyloxy-3-trimethylammonium propane (DOTAP)], we demonstrated in vivo by a single intravenous injection of DNA/liposome complexes into mice, that cationic liposomes are capable of transfecting cells in organs such as the lung, heart, liver, spleen, and kidney. Transfection efficiency is determined mainly by the structure of the cationic lipid and the ratio of cationic lipid to DNA. Although the presence of cholesterol in DOTAP liposomes did not affect transfection activity, inclusion of dioleoylphosphatidylethanolamine (DOPE) into either DOTAP or DOTMA liposomes significantly decreases liposome transfection activity in vivo. Results form time course show that gene expression in different organs is transient, with a peak level between 4 and 24 hr, dropping to less than 1% of the peak level by day 4. Experiments with repeated injections showed that the peak level of gene expression could be regained by subsequent injection.

Animals↗
PubMed1997

The dynamics of partially extended single molecules of DNA.

The behaviour of an isolated polymer floating in a solvent forms the basis of our understanding of polymer dynamics. Classical theories describe the motion of a polymer with linear equations of motion, which yield a set of 'normal modes', analogous to the fundamental frequency and the harmonics of a vibrating violin string. But hydrodynamic interactions make polymer dynamics inherently nonlinear, and the linearizing approximations required for the normal-mode picture have therefore been questioned. Here we test the normal-mode theory by measuring the fluctuations of single molecules of DNA held in a partially extended state with optical tweezers. We find that the motion of the DNA can be described by linearly independent normal modes, and we have experimentally determined the eigenstates of the system. Furthermore, we show that the spectrum of relaxation times obeys a power law.

Biopolymers↗
PubMed1997

Single polymer dynamics in an elongational flow.

The stretching of individual polymers in a spatially homogeneous velocity gradient was observed through use of fluorescently labeled DNA molecules. The probability distribution of molecular extension was determined as a function of time and strain rate. Although some molecules reached steady state, the average extension did not, even after a approximately 300-fold distortion of the underlying fluid element. At the highest strain rates, distinct conformational shapes with differing dynamics were observed. There was considerable variation in the onset of stretching, and chains with a dumbbell shape stretched more rapidly than folded ones. As the strain rate was increased, chains did not deform with the fluid element. The steady-state extension can be described by a model consisting of two beads connected by a spring representing the entropic elasticity of a worm-like chain, but the average dynamics cannot.

Bacteriophage lambda↗
PubMed1997

Bioreactive self-assembled monolayers on hydrogen-passivated Si(111) as a new class of atomically flat substrates for biological scanning probe microscopy.

This is the first report of bioreactive self-assembled monolayers, covalently bound to atomically flat silicon surfaces and capable of binding biomolecules for investigation by scanning probe microscopy and other surface-related assays and sensing devices. These monolayers are stable under a wide range of conditions and allow tailor-made functionalization for many purposes. We describe the substrate preparation and present an STM and SFM characterization, partly performed with multiwalled carbon nanotubes as tapping-mode supertips. Furthermore, we present two strategies of introducing in situ reactive headgroup functionalities. One method entails a free radical chlorosulfonation process with subsequent sulfonamide formation. A second method employs singlet carbenemediated hydrogen-carbon insertion of a heterobifunctional, amino-reactive trifluoromethyl-diazirinyl crosslinker. We believe that this new substrate is advantageous to others, because it (i) is atomically flat over large areas and can be prepared in a few hours with standard equipment, (ii) is stable under most conditions, (iii) can be modified to adjust a certain degree of reactivity and hydrophobicity, which allows physical adsorption or covalent crosslinking of the biological specimen, (iv) builds the bridge between semiconductor microfabrication and organic/biological molecular systems, and (v) is accessible to nanopatterning and applications requiring conductive substrates.

Alkanes↗
PubMed1997

Transepithelial SCFA gradients regulate polarized Na/H exchangers and pH microdomains in colonic epithelia.

Short chain fatty acids (SCFAs) stimulate electroneutral sodium absorption by activation of apical Na/H exchange in colonocytes. It is often assumed that activation of Na/H exchange is via an intracellular acidification caused by SCFA uptake. These lecture notes review shortcomings in this model of SCFA-stimulated sodium absorption, revealed by recent reports in the literature. This is supplemented by information generated in our laboratory using both a tissue culture model of colonocytes (HT29-C1 cells) and a native tissue preparation (mouse distal colonic mucosa). In both preparations, evidence suggests that physiologic SCFA gradients may generate pH heterogeneity in aqueous microdomains near the plasma membrane of colonocytes. Finally, direct observation of such extracellular microdomains with confocal microscopy is used to support a new model, in which pH microdomains play an important role in regulating both SCFA fluxes and sodium absorption.

Animals↗
PubMed1997

Transepithelial SCFA fluxes link intracellular and extracellular pH regulation of mouse colonocytes.

We have studied pH regulation in both intracellular and extracellular compartments of mouse colonic crypts, using distal colonic mucosa with intact epithelial architecture. In this work, we question how transepithelial SCFA gradients affect intracellular pH (pHi) and examine interactions between extracellular pH (pHo) and pHi regulation in crypts of distal colonic epithelium from mouse. We studied pH regulation in three adjacent compartments of distal colonic epithelium (crypt lumen, crypt epithelial cell cytosol, and lamina propria) with SNARF-1 (a pH sensitive fluorescent dye), digital imaging microscopy (for pHi), and confocal microscopy (for pHo). Combining results from the three compartments allows us to find how pHi and pHo are regulated and related under the influence of physiological transepithelial SCFA gradients, and develop a better understanding of pH regulation mechanisms in colonic crypts. Results suggest a complex interdependency between SCFA fluxes and pHo values, which can directly affect how strongly SCFAs acidify colonocytes.

Animals↗
PubMed1997

Influence of DNA sequence identity on efficiency of targeted gene replacement.

We have developed a system for analyzing recombination between a DNA fragment released in the nucleus from a single-copy plasmid and a genomic target in order to determine the influence of DNA sequence mismatches on the frequency of gene replacement in Saccharomyces cerevisiae. Mismatching was shown to be a potent barrier to efficient gene replacement, but its effect was considerably ameliorated by the presence of DNA sequences that are identical to the genomic target at one end of a chimeric DNA fragment. Disruption of the mismatch repair gene MSH2 greatly reduces but does not eliminate the barrier to recombination between mismatched DNA fragment and genomic target sequences, indicating that the inhibition of gene replacement with mismatched sequences is at least partially under the control of mismatch repair. We also found that mismatched sequences inhibited recombination between a DNA fragment and the genome only when they were close to the edge of the fragment. Together these data indicate that while mismatches can destabilize the relationship between a DNA fragment and a genomic target sequence, they will only do so if they are likely to be in the heteroduplex formed between the recombining molecules.

Base Sequence↗
PubMed1997

A novel protein shared by RNase MRP and RNase P.

We have isolated suppressors of the temperature-sensitive rRNA processing mutation rrp2-2 in Saccharomyces cerevisiae. A class of extragenic suppressors was mapped to the YBR257w reading frame in the right arm of Chromosome II. Characterization of this gene, renamed POP4, shows that the gene product is necessary both for normal 5.8S rRNA processing and for processing of tRNA. Immunoprecipitation studies indicate that Pop4p is associated with both RNase MRP and RNase P. The protein is also required for accumulation of RNA from each of the two ribonucleoprotein particles.

Amino Acid Sequence↗
PubMed1996

A short CIC-2 mRNA transcript is produced by exon skipping.

CIC-2 is a voltage- and volume-regulated chloride channel expressed in many tissues. We have shown that CIC-2 in rat lung airways is significantly down-regulated after birth [Murray,C.B. et al. (1995) Am. J. Respir. Cell Mol. Biol., 12, 597-604]. During PCR amplification from rat lung cDNA, a second transcript was identified which is 60 bp shorter than the full length sequence. The peptide translated from this 60 bp sequence contains many positively charged amino acid residues. Rat genomic DNA sequencing showed that the 60 bp sequence is an intact exon. A 71% pyrimidine content and an AAG 3'-end splice site in the intron immediately upstream from the 60 bp sequence were identified which may account for the alternative splicing of the following exon. Human genomic sequence analyses demonstrated similar intron-exon arrangement. A high CT content and an AAG 3' acceptor site were conserved in the intron corresponding to the rat upstream intron. The presence of the full length short form transcript was confirmed in rat kidney by RT-PCR, and the ratio of the long and the short form transcripts varied significantly according to the tissues examined, with the lowest long/short form ratio found in the lung among the tissues studied. Our data demonstrated that the alternatively spliced short form (CIC-2S) is transcribed in many rat tissues, the ratio of the long/short form transcripts is lower in the lung compared with the brain, and the genomic organization in this area is conserved in rat and human.

Alternative Splicing↗
PubMed1996

Non-ionic diffusion and carrier-mediated transport drive extracellullar pH regulation of mouse colonic crypts.

1. Extracellular pH (pHo) regulation within mouse colonic crypt lumens is stimulated by transepithelial gradients of short-chain fatty acids (SCFAs). Current work assesses underlying mechanisms contributing to pHo regulation. 2. Crypt luminal alkalinization was saturable by apical SCFA (substrate concentration activating half-maximal transport (KT) of isobutyrate = 45 mM). However, saturation was consistent with either carrier-mediated SCFA flux or non-ionic diffusion, because the non-ionized form was titrated by luminal alkalinization. Direct acidification of apical perfusates increased the magnitude of SCFA-induced luminal alkalinization, roughly in the same proportion to the increased concentration of non-ionized SCFA in the crypt lumen. 3. Transepithelial gradients of an alternative weak acid (CO2) produce pHo changes similar to SCFA. In contrast, a weak base (NH3) changes pHo with reverse dependence on the orientation of the transepithelial gradient compared with SCFA. Results implicate non-ionic diffusion in pHo regulation, and suggest that pHo changes may underly SCFA-stimulated bicarbonate secretion and ammonium absorption. 4. SCFA metabolism plays a minor role in extracellular pH regulation. An avidly metabolized SCFA (N-butyrate) augments crypt luminal alkalinization only slightly (0.08 pH units) versus a poorly metabolized SCFA (isobutyrate). 5. Apical addition of 1 mM 4,4'-diisothiocyanatostilbene-2,2'-disulphonic acid (DIDS) partially inhibits luminal alkalinization caused by apical SCFA. DIDS has no effect on luminal alkalinization caused by transepithelial CO2 gradients. Probenecid (1 mM), alpha-cyano-4-hydroxycinnamic acid (4 mM) or basolateral DIDS (1 mM) do not affect pHo regulation. Results suggest that DIDS-sensitive, SCFA-dependent transport in the colonocyte apical membrane contributes to pHo regulation.

4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid↗