Biomedical subjects

S Lin

Publications and source records attributed to S Lin.

At least 19 recordsLinked to original sources

PubMed1998

Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins.

We present evidence that a well defined subset of intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to retest two predictions of the theory that the first genes were constructed by exon shuffling. These predictions are that there should be an excess of symmetric exons (and sets of exons) flanked by introns of the same phase (positions within the codon) and that intron positions in ancient proteins should correlate with the boundaries of compact protein modules. Both these predictions are supported by the data, with considerable statistical force (P values < 0.0001). Intron positions correlate to modules of diameters around 21, 27, and 33 A, and this correlation is due to phase zero introns. We suggest that 30-40% of present day intron positions in ancient genes correspond to phase zero introns originally present in the progenote, while almost all of the remaining intron positions correspond to introns added, or moved, appearing equally in all three intron phases. This proposal provides a resolution for many of the arguments of the introns-early/introns-late debate.

Animals↗

PubMed1998

Modification of bacterial artificial chromosomes through chi-stimulated homologous recombination and its application in zebrafish transgenesis.

The modification of yeast artificial chromosomes through homologous recombination has become a useful genetic tool for studying gene function and enhancer/promoter activity. However, it is difficult to purify intact yeast artificial chromosome DNA at a concentration sufficient for many applications. Bacterial artificial chromosomes (BACs) are vectors that can accommodate large DNA fragments and can easily be purified as plasmid DNA. We report herein a simple procedure for modifying BACs through homologous recombination using a targeting construct containing properly situated Chi sites. To demonstrate a usage for this technique, we modified BAC clones containing the zebrafish GATA-2 genomic locus by replacing the first coding exon with the green fluorescent protein (GFP) reporter gene. Molecular analyses confirmed that the modification occurred without additional deletions or rearrangements of the BACs. Microinjection demonstrated that GATA-2 expression patterns can be recapitulated in living zebrafish embryos by using these GFP-modified GATA-2 BACs. Embryos microinjected with the modified BAC clones were less mosaic and had improved GFP expression in hematopoietic progenitor cells compared with smaller plasmid constructs. The precise modification of BACs through Chi-stimulated homologous recombination should be useful for studying gene function and regulation in cultured cells or organisms where gene transfer is applicable.

Animals↗

PubMed1998

Phosphatidylinositol-3,4,5-trisphosphate (PtdIns-3,4,5-P3)/Tec kinase-dependent calcium signaling pathway: a target for SHIP-mediated inhibitory signals.

Tec family non-receptor tyrosine kinases have been implicated in signal transduction events initiated by cell surface receptors from a broad range of cell types, including an essential role in B-cell development. A unique feature of several Tec members among known tyrosine kinases is the presence of an N-terminal pleckstrin homology (PH) domain. We directly demonstrate that phosphatidylinositol-3,4,5-trisphosphate (PtdIns-3,4,5-P3) interacting with the PH domain acts as an upstream activation signal for Tec kinases, resulting in Tec kinase-dependent phospholipase Cgamma (PLCgamma) tyrosine phosphorylation and inositol trisphosphate production. In addition, we show that this pathway is blocked when an SH2-containing inositol phosphatase (SHIP)-dependent inhibitory receptor is engaged. Together, our results suggest a general mechanism whereby PtdIns-3,4,5-P3 regulates receptor-dependent calcium signals through the function of Tec kinases.

Agammaglobulinaemia Tyrosine Kinase↗

PubMed1998

Mechanism of microsomal epoxide hydrolase. Semifunctional site-specific mutants affecting the alkylation half-reaction.

Microsomal epoxide hydrolase (MEH) catalyzes the addition of water to epoxides in a two-step reaction involving initial attack of an active site carboxylate on the oxirane to give an ester intermediate followed by hydrolysis of the ester. An efficient bacterial expression system for the enzyme from rat that facilitates the production of native and mutant enzymes for mechanistic analysis is described. Pre-steady-state kinetics of the native enzyme toward glycidyl-4-nitrobenzoates, 1, indicate the rate-limiting step in the reaction is hydrolysis of the alkyl-enzyme intermediate. The enzyme is enantioselective, turning over (2R)-1 about 10-fold more efficiently than (2S)-1, and regiospecific toward both substrates with exclusive attack at the least hindered oxirane carbon. Facile isomerization of the monoglyceride product is observed and complicates the regiochemical analysis. The D226E and D226N mutants of the protein are catalytically inactive, behavior that is consistent with the role of D226 as the active-site nucleophile as suggested by sequence alignments with other alpha/beta-hydrolase fold enzymes. The D226N mutant undergoes hydrolytic autoactivation with a half-life of 9.3 days at 37 degreesC, suggesting that the mutant is still capable of catalyzing the hydrolytic half-reaction (in this instance an amidase reaction) and confirming that D226 is in the active site. The indoylyl side chain of W227, which is in or near the active site, is not required for efficient alkylation of the enzyme or for hydrolysis of the intermediate. However, the W227F mutant does exhibit altered stereoselectivity toward (2R)-1, (2S)-1, and phenanthrene-9,10-oxide, suggesting that modifications at this position might be used to manipulate the stereo- and regioselectivity of the enzyme.

Alkylation↗

PubMed1998

Photoaffinity labeling by 4-thiodideoxyuridine triphosphate of the HIV-1 reverse transcriptase active site during synthesis. Sequence of the unique labeled hexapeptide.

The active site of HIV-1 reverse transcriptase (HIV-1 RT) was investigated by photoaffinity labeling based on catalytic competence. A stable ternary elongation complex was assembled containing enzyme, DNA template (RT20), DNA primer molecule (P12), and the necessary dNTPs (one of which was alpha-32P-labeled) needed for primer elongation. The photoaffinity probe 4-thiodideoxyuridine triphosphate was incorporated uniquely at the 3' terminus of the 32P-labeled DNA product. Upon photolysis, the p66 subunit of a HIV-1 RT heterodimer (p66/p51) was uniquely cross-linked to the DNA product and subsequently digested by either trypsin or endoproteinase Lys-C. The labeled HIV-1 RT peptide was separated, purified, and finally subjected to Edman microsequencing. A unique radioactive hexapeptide (V276RQLCK281) was identified and sequenced. Our photoaffinity labeling results were positioned on the HIV-1 RT. DNA.Fab complex x-ray crystallography structure and compared with the suggested aspartic triad active site.

Binding Sites↗

PubMed1998

Pre- and postnatal exposure to 3,3',4,4'-tetrachlorobiphenyl: II. Effects on the reproductive capacity and fertilizing ability of eggs in female mice.

This study investigated the effects of 3,3',4,4'-tetrachlorobiphenyl (TCB) on the reproductive capacity of female mice. Female C57BL/6J mice (F-0) were fed diets containing 0, 3, or 30 ppm TCB for 2 weeks before pairing with nontreated C57BL/6J males for a 10-day breeding period. Females were continued on their treatment diet throughout mating, gestation, and lactation. Female offspring (F-1) were fed the same diet as their dams throughout the study. The reproductive capacity of F-1 females was examined by mating with non-treated B6D2-F1 males. In addition, the fertilizing ability of eggs from F-1 females was examined in vitro by insemination with sperm from nontreated B6D2-F1 males. Fecundity in F-0 females after mating was 80%, 71%, and 47% in the 0, 3, and 30 ppm treatment groups, respectively. Four-day and 21-day survival indices were lower for offspring of 30 ppm TCB-treated F-0 females than for offspring of the control females. Fecundity in F-1 females was the same among all treatment groups, however, all offspring born to 3- and 30-ppm TCB-treated F-1 females died before 4 days of age. Although the litter size at birth was not affected, the in vitro fertilizing ability of eggs in the 3- and 30-ppm treatment groups was lower than in the control group. This decrease in fertilizing ability was associated with an increase in degenerated eggs. F-0 females treated with 30 ppm TCB had enlarged livers during pregnancy and lactation. At 5 and 6 weeks, liver enlargement and thymus atrophy were apparent in F-1 females exposed to 30 ppm TCB. This study demonstrated impaired reproductive capacity and decreased egg fertilizing ability in TCB-treated female mice.

Animals↗

PubMed1998

Tetravinyl-tetramethylcyclo-tetrasiloxane (tetravinyl D4) is a mutagen in Rat2lambda lacI fibroblasts.

Small fragments of silicone gels injected intraperitoneally have been used to induce plasmacytomas in genetically susceptible mice. Silicone oils, in contrast to silicone gels, are apparently not tumorigenic in the mouse plasmacytoma system. The reason for this difference as well as the mechanism of silicone gel-induced plasmacytoma development is poorly understood. We chose to examine the possibility that low molecular wt silicone compounds such as siloxanes, leaking from the complex silicone gel matrix into the surrounding tissue, may be mutagenic. We postulate that this mutagenicity may be a critical determinant of the plasmacytoma inducing potency of silicone gels. Six siloxane compounds, either linear or cyclic di-, tri-, or tetrasiloxanes substituted with methyl or vinyl moieties, were selected as model compounds to study mutagenicity in Rat2lambda lacI fibroblasts in vitro. Using phage lambda-derived lacI/lacZ genes as target/reporter genes to quantitate mutagenesis, and gamma-cyclodextrin as vehicle to effectively deliver siloxanes, we found that exposure to 50 microM of tetravinyl-tetramethylcyclo-tetrasiloxane (tetravinyl D4) resulted in a modest 1.7-fold increase of mutant frequencies over controls in Rat2lambda lacI cells. In related toxicity experiments, tetravinyl D4 was shown to perturb lipid membranes leading to a loss of cytosolic glutathione (GSH), which by itself resulted in a 1.5-fold increased mutant rate in Rat2lambda lacI cells. We conclude that certain siloxanes may act as direct mutagens in mammalian cells. In addition, siloxane-induced mutagenicity may be enhanced by the depletion of intracellular GSH caused by the interaction of lipophilic siloxanes with cell membranes.

Animals↗

PubMed1997

Preliminary results from intensity-based CT-SPECT fusion in I-131 anti-B1 monoclonal-antibody therapy of lymphoma.

BACKGROUND: In treatment of non-Hodgkin's lymphoma patients with predose-plus-I-131-labeled anti-B1 (anti-CD20) monoclonal antibody, an intratherapy single photon emission computed tomography (SPECT) image is an important part of research estimates of tumor dosimetry. For that imaging, a computed tomography (CT)-SPECT fusion is used both to obtain an attenuation map for the space-alternating generalized expectation maximization reconstruction and to provide CT-based volumes of interest (VoI) to determine activity in tumors and organs. Fusion based on external, skin-surface markers has been used but may not correctly superimpose internal structures. METHODS: A new algorithm, developed and implemented in the Department of Radiology, University of Michigan, and based on the mutual information of grayscale values, was investigated. Results from four anti-B1 therapy patients are presented. RESULTS: In one patient, the new intensity-based fusion provided total reconstructed counts for kidneys that were higher than those produced by marker-based fusion; therefore, the VoI was probably located more accurately. In a second patient, after an acquisition that did not include any skin markers, the new algorithm produced counts/pixel that were similar for four of five tumors consistent with what is expected from an ideal therapy combined with accurate count density estimates. The fifth tumor was quite small and will have its final activity estimate moved toward consistency with the others after a recovery coefficient multiplication. For four tumors in two patients, direct comparison of the two algorithms yielded count totals that were different by no more than 7.2%. CONCLUSIONS: The use of CT-SPECT fusion and subsequent transfer of tumor VoI originally drawn in high-resolution CT space offers potential advantages for quantifying tumor uptake of radioactivity. A new, mutual-information-based fusion algorithm is usable without skin markers. Results indicate that the new fusion algorithm gives equal tumor count values within 7.2% compared with fusion based on external markers. It increases estimates of kidney activity by an average of 6.4%.

Algorithms↗

PubMed1997

Determination of the dissociation constant of phosvitin-anti-phosphoserine interaction by affinity capillary electrophoresis.

We used affinity capillary electrophoresis (ACE) to study the interaction of a monoclonal anti-phosphoserine antibody (mAb) to a homopolyvalent antigen (hpAg), phosvitin. A model system, which allows the measurement of the true dissociation constant (Kd) in Ag excess based on measurement of migration shifts of mAb-hpAg complexes at different Ag concentrations in solution, is presented for the study of the interactions between a mAb and an Ag that has identical determinants. The experimental value of Kd (22.4 x 10(-6) M) obtained by ACE is shown to be in close agreement with the value (17.8 x 10(-6) M) obtained by the conventional immunoassay based on indirect competition enzyme-linked immunosorbent assay (ELISA). Moreover, the Kds of mAb-hpAg complexes were measured and shown to be independent of the applied electrical field strength. Thus, under conditions where the total Ag concentration is in large excess over the total Ab concentration and when certain requirements are fulfilled, this method offers the advantage of dealing with the determination of Kd for unlabeled mAb and homopolymeric Ag molecules in free solution rather than at the liquid-solid interface.

Antibodies, Monoclonal↗

PubMed1997

Site-specific fluorescence labeling of the beta2 adrenergic receptor amino terminus.

A modified human beta2 receptor, designated 0K-beta2, was developed for site-specific labeling at the amino terminus with amine reactive fluorescent probes. 0K-beta2 has the following modifications: (1) all 16 lysines in the wild-type beta2 receptor were mutated to arginines, (2) a FLAG epitope preceded by a cleaved hemagglutinin signal sequence was fused to the amino terminus, and (3) a hexahistidine tail was added to the carboxyl terminus. The FLAG epitope and hexahistidine tail were added to facilitate purification while lysine to arginine mutations eliminate potential labeling sites for amine-reactive fluorescent probes. The remaining primary amines in the 0K-beta2 receptor, the amino terminal amine and the epsilon-amine of Lys3, both reside in the amino-terminal FLAG epitope. The 0K-beta2 receptor expressed in Sf9 insect cells exhibited ligand binding and G-protein coupling characteristics similar to the wild-type beta2 receptor. The modified receptor was labeled with fluorescamine, an amine-reactive fluorescent probe. Proteolysis with factor Xa showed that labeling was confined to the amino terminus of the 0K-beta2 receptor. Our results demonstrate site-specific fluorescamine labeling at the amino terminus of the 0K-beta2 receptor, a lysine-depleted beta2 receptor that retains functional characteristics of the wild-type receptor.

Adenylyl Cyclases↗

PubMed1997

Agonists induce conformational changes in transmembrane domains III and VI of the beta2 adrenoceptor.

Agonist binding to G protein-coupled receptors is believed to promote a conformational change that leads to the formation of the active receptor state. However, the character of this conformational change which provides the important link between agonist binding and G protein coupling is not known. Here we report evidence that agonist binding to the beta2 adrenoceptor induces a conformational change around 125Cys in transmembrane domain (TM) III and around 285Cys in TM VI. A series of mutant beta2 adrenoceptors with a limited number of cysteines available for chemical derivatization were purified, site-selectively labeled with the conformationally sensitive, cysteine-reactive fluorophore IANBD and analyzed by fluorescence spectroscopy. Like the wild-type receptor, mutant receptors containing 125Cys and/or 285Cys showed an agonist-induced decrease in fluorescence, while no agonist-induced response was observed in a receptor where these two cysteines were mutated. These data suggest that IANBD bound to 125Cys and 285Cys are exposed to a more polar environment upon agonist binding, and indicate that movements of transmembrane segments III and VI are involved in activation of G protein-coupled receptors.

Adrenergic beta-Agonists↗

PubMed1997

Fasting increases leptin receptor mRNA expression in lean but not obese (ob/ob) mouse brain.

Using a non-radioactive in situ hybridization detection method, we found that fasting up-regulated leptin receptor mRNA expression in the brain of C57 Bl/6 lean (+/+) but not obese (ob/ob) mice. After the lean mice were fasted for 24 h, increased leptin receptor mRNA expression was found in the arcuate and ventromedial hypothalamic nuclei, medial habenular nucleus and dentate gyrus of hippocampal formation. There was only a minor increase in mRNA expression of leptin receptor in the hippocampus proper while the piriform cortex remained unchanged. However, after the obese mice were fasted for 24 h, no detectable changes of leptin receptor mRNA expression could be found. These results indicated that leptin receptor gene expression was influenced by nutritional status. Further, genetically obese mice showed an inability to respond to nutritional change, probably due to the fact that obese mice lack leptin.

Animals↗

PubMed1997

Tyrosine-dependent basolateral sorting signals are distinct from tyrosine-dependent internalization signals.

Converting cysteine 543 to tyrosine in the influenza virus hemagglutinin (HA) introduces both a basolateral sorting signal and an internalization signal into the HA cytoplasmic domain. Another HA mutant, HA+8, contains eight additional amino acids at the end of the cytoplasmic domain that include a powerful internalization signal. HA+8 was also sorted efficiently to the basolateral surface of Madin-Darby canine kidney cells. The simplest explanation for the observation that multiple sorting phenotypes depend upon the same small amino acid sequence is that certain tyrosine-based internalization signals might also function as basolateral sorting signals. To test this hypothesis, second-site mutations were introduced into HA C543Y or HA+8 to determine if the internalization and basolateral sorting functions can be separated. For HA C543Y, the same sequence positions were important for both basolateral sorting and internalization, but the two functions responded differently to individual amino acid replacements, indicating that they were distinct. For HA+8, the basolateral sorting signal required the same tyrosine as the internalization signal, but did not share any other characteristics. Thus, even when basolateral sorting signals that depend on tyrosine overlap or are co-linear with internalizations signals, the two sorting processes are sensitive to different characteristics of the sequence.

Amino Acid Sequence↗

PubMed1997

Promoter analysis in living zebrafish embryos identifies a cis-acting motif required for neuronal expression of GATA-2.

We have used zebrafish embryos to dissect the promoter activity of a gene with a complex expression pattern during embryogenesis. GATA-2 is a transcription factor required for hematopoiesis and is dynamically expressed in hematopoietic tissues and in the central nervous system. Using constructs containing zebrafish GATA-2 genomic flanking sequences and the green fluorescent protein (GFP) reporter gene, we demonstrate that distinct regulatory domains are required for hematopoietic, enveloping layer (EVL), and neuronal expression of GATA-2. During gastrulation, GFP expression is confined to the ventral ectoderm and lateral mesoderm and is lacking in the dorsal shield. Cells derived from the regions expressing GFP give rise to hematopoietic progenitors, EVL cells, and neurons. Deletion analysis of the 7.3-kb GATA-2 promoter region revealed that a 1.1-kb DNA sequence is critical for expression of GATA-2 in neurons. Fine mapping revealed that a 31-bp region is required for neuron enhancer activity, and mutagenesis showed that the DNA motif CCCTCCT is essential for GATA-2 promoter activity in the central nervous system of zebrafish. Our use of zebrafish embryos can be exploited as a whole animal system for the dissection of any developmentally regulated vertebrate promoter.

Animals↗

PubMed1997

Blockade of the voltage-gated potassium channel Kv1.3 inhibits immune responses in vivo.

The voltage activated K+ channel (Kv1.3) has recently been identified as the molecule that sets the resting membrane potential of peripheral human T lymphoid cells. In vitro studies indicate that blockage of Kv1.3 inhibits T cell activation, suggesting that Kv1.3 may be a target for immunosuppression. However, despite the in vitro evidence, there has been no in vivo demonstration that blockade of Kv1.3 will attenuate an immune response. The difficulty is due to species differences, as the channel does not set the membrane potential in rodent peripheral T cells. In this study, we show that the channel is present on peripheral T cells of miniswine. Using the peptidyl Kv1.3 inhibitor, margatoxin, we demonstrate that Kv1.3 also regulates the resting membrane potential, and that blockade of Kv1.3 inhibits, in vivo, both a delayed-type hypersensitivity reaction and an Ab response to an allogeneic challenge. In addition, prolonged Kv1.3 blockade causes reduced thymic cellularity and inhibits the thymic development of T cell subsets. These results provide in vivo evidence that Kv1.3 is a novel target for immunomodulation.

Animals↗

PubMed1997

Syntheses of 1,2-di-O-palmitoyl-sn-glycero-3-phosphocholine (DPPC) and analogs with 13C- and 2H-labeled choline head groups.

The syntheses of four head group labeled analogs of 1,2-di-O-palmitoyl-sn-glycero-3-phosphocholine (DPPC) (6) by a general method from 1,2-di-O-palmitoyl-sn-glycero-3-phosphatidic acid (5) have been performed. The syntheses of 1,2-di-O-palmitoyl-sn-glycero-3-phospho[alpha-13C]choline (6a) and 1,2-di-O-palmitoyl-sn-glycero-3-phospho[beta-13C]choline (6b) were performed from labeled [1-13C]glycine (1a) in 52% overall yield and from [2-13C]glycine (1b) in 56% overall yield, respectively. 1,2-Di-O-palmitoyl-sn-glycero-3-phospho[N(C2H3)3]choline (9) was prepared from 2-aminoethanol in 39% overall yield. 1,2-Di-O-palmitoyl-sn-glycero-3-phospho[alpha-C2H2]choline (12) was prepared from N,N-dimethylglycine ethyl ester in 50% overall yield.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1997

Self-organization of firing activities in monkey's motor cortex: trajectory computation from spike signals.

The population vector method has been developed to combine the simultaneous direction-related activities of a population of motor cortical neurons to predict the trajectory of the arm movement. In this article, we consider a self-organizing model of a neural representation of the arm trajectory based on neuronal discharge rates. As self-organizing feature map (SOFM) is used to select the optimal set of weights in the model to determine the contribution of an individual neuron to an overall movement representation. The correspondence between movement directions and discharge patterns of the motor cortical neurons is established in the output map. The topology-preserving property of the SOFM is used to analyze the recorded data of a behaving monkey. The data used in this analysis were taken while the monkey was tracing spirals and doing center-->out movements. The arm trajectory could be well predicted using such a statistical model based on the motor cortex neuronal firing information. The SOFM method is compared with the population vector method, which extracts information related to trajectory by assuming that each cell has a fixed preferred direction during the task. This implies that these cells are acting along lines labeled only for direction. However, extradirectional information is carried in these cell responses. The SOFM has the capability of extracting not only direction-related information but also other parameters that are consistently represented in the activity of the recorded population of cells.

Algorithms↗

PubMed1997

Specific mutation near the primary donor in photosystem I from Chlamydomonas reinhardtii alters the trapping time and spectroscopic properties of P700.

Time-resolved absorption and fluorescence spectroscopy were used to investigate the energy and electron transfer processes in the detergent-isolated photosystem I core particles from the site-directed mutant of Chlamydomonas reinhardtii with the histidine-656 of PsaB replaced by asparagine [HN(B656) mutation]. The specific mutation near the primary donor molecule results in a 40 mV increase in the P700/P700+ midpoint potential [Webber, A. N., Su Hui, Bingham, S. E., Kass, H., Krabben, L., Kuhn, M., Jordan, R., Schlodder, E., & Lubitz, W. (1996) Biochemistry 35, 12857-12863]. There is no indication that the HN(B656) mutation affects the spectral distribution of the antenna pigments. However, the lifetime of the trapping process measured independently by transient absorption and fluorescence spectroscopy in the mutant PSI core antenna is increased by a factor of approximately 2 (approximately 65 ps compared to approximately 30 ps in the wild-type PSI). This implies that the trapping process in the PSI antenna is limited by the process where the primary donor molecule directly participates. The HN(B656) mutation results in the appearance of a new bleaching band at 670 nm in the spectrum which is due to formation of P700+ upon photooxidation. The difference spectrum of the photoreduction of the possible primary acceptor, A0 in the mutant PSI is very similar to wild type, indicating that it is unaffected by the HN(B656) mutation. Possible mechanisms for slowing of the trapping process and the appearance of a new band in the P700 - P700+ difference spectrum of the HN(B656) PSI are discussed.

Animals↗