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Biomedical subjects

J C Liao

Publications and source records attributed to J C Liao.

At least 19 recordsLinked to original sources
PubMed2001

Acetate-inducible protein overexpression from the glnAp2 promoter of Escherichia coli.

The Ntr regulon in Escherichia coli has previously been engineered to control the expression of a heterologous metabolic pathway. In this study, we reengineered the same system for protein production. In the absence of NRII (glnL gene product), we showed that glnAp2 can be an effective promoter for protein production that is inducible by exogenous acetate, but both the induction ratio and the range of modulation are low. To deal with this issue, we inactivated phosphotransacetylase (pta gene product), which disrupts the acetate pathway and denies the cell the ability to synthesize acetate. With this additional modification, gene expression from glnAp2 can be controlled by directly adding acetate into the growth medium. Using a lacZ reporter fusion, we found that glnAp2 induction was modulatable over a range of potassium acetate concentrations, and the induction/noninduction ratio increased to 77 in the absence of pta. The extracellular acetate required for maximal induction is lower than the concentration that causes toxicity, and thus growth inhibition by acetate addition was not a matter of concern. Furthermore, compared to the P(tac) promoter, overexpression of a model protein using the modified glnAp2 promoter system did not cause significant growth inhibition, although a higher level of protein expression was achieved.

Acetic Acid↗
PubMed2001

Modulation of nitric oxide bioavailability by erythrocytes.

Nitric oxide (NO) activates soluble guanylyl cyclase in smooth muscle cells to induce vasodilation in the vasculature. However, as hemoglobin (Hb) is an effective scavenger of NO and is present in high concentrations inside the red blood cell (RBC), the bioavailability of NO would be too low to elicit soluble guanylyl cyclase activation in the presence of blood. Therefore, NO bioactivity must be preserved. Here we present evidence suggesting that the RBC participates in the preservation of NO bioactivity by reducing NO influx. The NO uptake by RBCs was increased and decreased by altering the degree of band 3 binding to the cytoskeleton. Methemoglobin and denatured hemoglobin binding to the RBC membrane or cytoskeleton also were shown to contribute to reducing the NO uptake rate of the RBC. These alterations in NO uptake by the RBC, hence the NO bioavailability, were determined to correlate with the vasodilation of isolated blood vessels. Our observations suggest that RBC membrane and cytoskeleton associated NO-inert proteins provide a barrier for NO diffusion and thus account for the reduction in the NO uptake rate of RBCs.

4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid↗
PubMed2001

Alteration of product specificity of Rhodobacter sphaeroides phytoene desaturase by directed evolution.

Phytoene desaturases occurring in nature convert phytoene to either neurosporene or lycopene in most eubacteria. Approximately 10% of known phytoene desaturases, as in Rhodobacter, produce neurosporene, whereas the rest produce lycopene. These two types of enzymes, although similar in function, have relatively low similarity (below 60%) in terms of nucleotide or amino acid sequence. The mechanism controlling the product specificity of these enzymes is unclear. Here we used directed evolution to change the product of Rhodobacter sphaeroides phytoene desaturase (crtI gene product), a neurosporene-producing enzyme, to lycopene. Two generations of random mutagenesis were performed, from which three positive mutants were isolated and sequenced. We then used site-directed mutagenesis to determine the effect of each amino acid change. Gathering information from random mutagenesis, we further recombined the beneficial mutations by site-directed mutagenesis and increased the percent of lycopene production to 90%.

Base Sequence↗
PubMed2001

Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.

We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the same slide, to filter out outlying spots, poor quality genes and problematical slides. We also perform calibration experiments to show that normalization between fluorescent labels is needed and that the normalization is slide dependent and non-linear. A rank invariant method is suggested to select non-differentially expressed genes and to construct normalization curves in comparative experiments. After normalization the residuals from the calibration data are used to provide prior information on variance components in the analysis of comparative experiments. Based on a hierarchical model that incorporates several levels of variations, a method for assessing the significance of gene effects in comparative experiments is presented. The analysis is demonstrated via two groups of experiments with 125 and 4129 genes, respectively, in Escherichia coli grown in glucose and acetate.

Acetic Acid↗
PubMed2001

Macrophage arginase promotes tumor cell growth and suppresses nitric oxide-mediated tumor cytotoxicity.

Macrophages use L-arginine to synthesize nitric oxide (NO) and polyamines through the inducible NO synthase (iNOS) and arginase, respectively. The released NO contributes to the tumoricidal activity of macrophages, whereas polyamines may promote the growth of tumor cells. Both the tumoricidal and growth-promoting activities from macrophages have been reported; however, the underlying mechanisms for switching between this dual function of macrophages remain unclear. Here, we test the hypothesis that arginase participates in the switching between the cytotoxic and growth-promoting activities of macrophages toward tumor cells. To alter arginase activity in macrophages, cells (murine macrophage cell line J774A.1) were transfected with the rat liver arginase gene or treated with an arginase inhibitor, L-norvaline. The effects of macrophage arginase activity on the growth-promoting and cytotoxic activities of macrophages toward breast tumor cells (ZR-75-1) were investigated in a coculture system. The results demonstrated that overexpression of arginase in macrophages enhanced L-ornithine and putrescine production and consequently promoted tumor cell proliferation. This proliferative effect was down-regulated by the arginase inhibitor L-norvaline. Furthermore, increases in arginase activity also attenuated NO production by the lipopolysaccharide-activated macrophages and thus reduced the cytotoxic effect on cocultured tumor cells. Inhibiting arginase activity by L-norvaline effectively reversed the suppression of NO-mediated tumor cytotoxicity. Together, these results suggest that arginase induction in macrophages can enhance tumor cell growth by providing them with polyamines and suppress tumor cytotoxicity by reducing NO production. It appears that L-arginine metabolism through the arginase and iNOS pathways in macrophages can have very different influences on the growth of nearby tumor cells depending on which pathway is prevailing.

Adenocarcinoma↗
PubMed2001

Metabolic engineering of isoprenoids.

The metabolic engineering of natural products has begun to prosper in the past few years due to genomic research and the discovery of biosynthetic genes. While the biosynthetic pathways and genes for some isoprenoids have been known for many years, new pathways have been found and known pathways have been further investigated. In this article, we review the recent advances in metabolic engineering of isoprenoids, focusing on the molecular genetics that affects pathway engineering the most. Examples in mono- sequi-, and diterpenoid synthesis as well as carotenoid production are discussed.

Carbohydrate Sequence↗
PubMed2001

Erythrocyte consumption of nitric oxide: competition experiment and model analysis.

It is generally believed that the erythrocyte membrane is highly permeable to nitric oxide (NO). To prevent NO from freely entering and being scavenged by the red blood cell (RBC), it has been suggested that NO consumption is limited by the mass transfer resistance of the diffusion layer adjacent to the erythrocyte membrane. Recently, we (Vaughn et al. (2000). J. Biol. Chem. 275, 2342) presented an experimental technique that overcomes experimental diffusional limitations and showed that RBCs also possess a mechanism to slow nitric oxide uptake. Here, we present a mathematical analysis of this technique by modeling the NO uptake of a single cell. We obtain additional data (n = 33, total) by use of the competition experiment and, through application of the model, show that either the RBC membrane permeability to NO or the intracellular reaction rate between NO and hemoglobin (Hb) is at least 2000-fold lower than previously thought. As a result, RBCs react with NO at a rate three orders of magnitude slower than free oxyHb. This phenomena may play an important role in NO bioavailability.

Animals↗
PubMed2001

Pediatric urine testing.

Today, urinalysis is one of the most common clinical tests ordered for adult and pediatric patients. Because urine specimens are usually readily available and are obtained noninvasively, the urine testing is well suited for children. This article discusses the most common urine tests performed in children for screening purposes and also less common tests for diagnosis of specific disorders. Special considerations regarding urine specimen collection in children are discussed. Some simple tests that are underused by clinicians are mentioned, as are some exciting new molecular applications of urine testing.

Child↗
PubMed2001

Neonatal circumcision.

The merits of neonatal circumcision continue to be debated hotly. Some argue that circumcision is a "uniquely American medical enigma." Most of the world's male population remains uncircumcised; however, most boys born in the United States continue to undergo neonatal circumcision. Review of existing literature supports that most children who are uncircumcised do well from a medical standpoint and, thus, the question of whether US health care practitioners are subjecting neonates to an unnecessary surgical procedure remains. The medical benefits of circumcision are multiple, but most are small. The clearest medical benefit of circumcision is the relative reduction in the risk for a UTI, especially in early infancy. Although this risk [figure: see text] is real, the absolute numbers are small (risk ranges from 1 in 100 to 1 in 1000), and one investigator has estimated that it may take approximately 80 neonatal circumcisions to prevent one UTI. In the case of a patient with known urologic abnormalities that predispose to UTI, neonatal circumcision has a clearer role in terms of medical benefit to the patient. Most of the other medical benefits of circumcision probably can be realized without circumcision as long as access to clean water and proper penile hygiene are achieved. Proper penile hygiene should all but eliminate the risk for foreskin-related medical problems that will require circumcision. Moreover, proper hygiene and access to clean water has been shown to reduce the rate of development of squamous cell carcinoma of the penis in the uncircumcised population. Proper techniques on the care of the foreskin are illustrated in the American Academy of Pediatrics pamphlet titled "How to care for the uncircumcised penis." Regarding the relationship between STDs and circumcision, patient education and the practice of low-risk sexual behavior make a far greater impact than does routine circumcision in hopes of reducing the spread of HIV and other STDs. Nevertheless, in areas where safe sexual practices are poorly adhered to, circumcision can have a relative protective effect against the transmission of HIV and other STDs. The medical harms of circumcision lie mainly in the 1% acute complication rate and the additional patients who require revision of their initial circumcision for cosmetic or medical reasons. Anecdotally, the authors see far fewer complications in the acute and long-term phase when the circumcision has been performed by someone with expertise and experience with the procedure. Thus, the authors routinely recommend to parents that, if they choose to have their newborns circumcised, they should seek out an experienced practitioner. A negative psychologic and sexual impact of circumcision has been argued, but solid, scientific data are lacking. Special interest groups have argued that perhaps the greatest harm of circumcision is in performing an operation without a clear indication. Many of these groups have claimed that performing a routine neonatal circumcision is akin to performing a surgical procedure without a clear medical benefit, and in an infant, that is akin to surgery without informed consent. Although this is an extreme posture, the clinician can understand the emphasis on trying to provide invasive medical services only when a clear medical benefit is expected, especially when treating an infant or child. Deciding whether or not to circumcise an infant continues to challenge many new parents. Clearly, the procedure provides potential medical benefits and potential risks. It is difficult to say whether the benefits outweigh the risks for all male infants. Further complicating the decision for many American parents is that, in some areas of the United States, there exists an unexplained positive cultural connotation with neonatal circumcision. For these reasons, parents who actively choose to keep their sons uncircumcised need to be encouraged to make this decision forthrightly. Parents who choose to have their children circumcised also should be encouraged to actively seek an experienced practitioner who can afford the child adequate local analgesia.

Analgesia↗
PubMed2001

Microbial pathway engineering for industrial processes: evolution, combinatorial biosynthesis and rational design.

Microbial pathway engineering has made significant progress in multiple areas. Many examples of successful pathway engineering for specialty and fine chemicals have been reported in the past two years. Novel carotenoids and polyketides have been synthesized using molecular evolution and combinatorial strategies. In addition, rational design approaches based on metabolic control have been reported to increase metabolic flux to specific products. Experimental and computational tools have been developed to aid in design, reconstruction and analysis of non-native pathways. It is expected that a hybrid of evolutionary, combinatorial and rational design approaches will yield significant advances in the near future.

Carotenoids↗
PubMed2000

The involvement of tyrosine kinases, cyclic AMP/protein kinase A, and p38 mitogen-activated protein kinase in IL-13-mediated arginase I induction in macrophages: its implications in IL-13-inhibited nitric oxide production.

In macrophages, L-arginine can be used by NO synthase and arginase to form NO and urea, respectively. Therefore, activation of arginase may be an effective mechanism for regulating NO production in macrophages through substrate competition. Here, we examined whether IL-13 up-regulates arginase and thus reduces NO production from LPS-activated macrophages. The signaling molecules involved in IL-13-induced arginase activation were also determined. Results showed that IL-13 increased arginase activity through de novo synthesis of the arginase I mRNA and protein. The activation of arginase was preceded by a transient increase in intracellular cAMP, tyrosine kinase phosphorylation, and p38 mitogen-activated protein kinase (MAPK) activation. Exogenous cAMP also increased arginase activity and enhanced the effect of IL-13 on arginase induction. The induction of arginase was abolished by a protein kinase A (PKA) inhibitor, KT5720, and was down-regulated by tyrosine kinase inhibitors and a p38 MAPK inhibitor, SB203580. However, inhibition of p38 MAPK had no effect on either the IL-13-increased intracellular cAMP or the exogenous cAMP-induced arginase activation, suggesting that p38 MAPK signaling is parallel to the cAMP/PKA pathway. Furthermore, the induction of arginase was insensitive to the protein kinase C and p44/p42 MAPK kinase inhibitors. Finally, IL-13 significantly inhibited NO production from LPS-activated macrophages, and this effect was reversed by an arginase inhibitor, L-norvaline. Together, these data demonstrate for the first time that IL-13 down-regulates NO production through arginase induction via cAMP/PKA, tyrosine kinase, and p38 MAPK signalings and underline the importance of arginase in the immunosuppressive activity of IL-13 in activated macrophages.

Animals↗
PubMed2000

Erythrocytes possess an intrinsic barrier to nitric oxide consumption.

It has been reported that free hemoglobin (Hb) reacts with NO at an extremely high rate (K(Hb) approximately 10(7) M(-1) s(-1)) and that the red blood cell (RBC) membrane is highly permeable to NO. RBCs, however, react with NO 500-1000 times slower. This reduction of NO reaction rate by RBCs has been attributed to the extracellular diffusion limitation. To test whether additional limitations are also important, we designed a competition test, which allows the extracellular diffusion limitation to be distinguished from transmembrane or intracellular resistance. This test exploited the competition between free Hb and RBCs for NO generated in a homogenous phase by an NO donor. If the extracellular diffusion resistance is negligible, then the results would follow a kinetic model that assumes homogenous reaction without extracellular diffusion limitation. In this case, the measured effective reaction rate constant, K(RBC), would remain invariant of the hematocrit, extracellular-free Hb concentration, and NO donor concentration. Results show that the K(RBC) approaches a constant only when the hematocrit is greater than 10%, suggesting that at higher hematocrit, the extracellular diffusion resistance is negligible. Under such a condition, the NO consumption by RBCs is still 500-1000 times slower than that by free Hb. This result suggests that intrinsic RBC factors, such as transmembrane diffusion limitation or intracellular mechanisms, exist to reduce the NO consumption by RBCs.

Animals↗
PubMed2000

DNA microarray detection of metabolic responses to protein overproduction in Escherichia coli.

It has been commonly observed that gratuitous overexpression of proteins in Escherichia coli causes growth retardation. However, the molecular events involved in the metabolic response to the over-expression of proteins are still unclear. Here we used DNA microarray technology to characterize the changes in transcriptional patterns of selected host genes during protein overexpression. A nontoxic, soluble protein, LuxA (coded by luxA), which is the alpha-subunit of the luciferase heterodimer, was overexpressed for this purpose. A total of 132 E. coli genes, including those in the central metabolism, key biosynthetic pathways, and selected regulatory functions, were used as probes for detecting the level of mRNA transcripts in E. coli strains JM109, MC4100, and VJS676A during protein overexpression. Upon induction, these strains shared several common responses, such as the upregulation of glk and the heat shock genes as well as the downregulation of fba, ppc, atpA, and gnd. In addition, the biosynthesis genes glnA, glyA, and leuA were downregulated in all three strains. Media-dependent responses were also observed in our study. For example, many respiratory genes that were upregulated in defined media showed an opposite effect in complex media under protein-overproducing conditions. These results demonstrate that gratuitous overexpression of proteins triggers a complex global response that involves several metabolic and regulatory systems. Explanations based on either existing knowledge of global regulations such as the heat shock response and the stringent response or stoichiometric analysis without regulatory considerations cannot account for the response induced by protein overexpression.

Bacterial Proteins↗
PubMed2000

Improving lycopene production in Escherichia coli by engineering metabolic control.

Metabolic engineering has achieved encouraging success in producing foreign metabolites in a variety of hosts. However, common strategies for engineering metabolic pathways focus on amplifying the desired enzymes and deregulating cellular controls. As a result, uncontrolled or deregulated metabolic pathways lead to metabolic imbalance and suboptimal productivity. Here we have demonstrated the second stage of metabolic engineering effort by designing and engineering a regulatory circuit to control gene expression in response to intracellular metabolic states. Specifically, we recruited and altered one of the global regulatory systems in Escherichia coli, the Ntr regulon, to control the engineered lycopene biosynthesis pathway. The artificially engineered regulon, stimulated by excess glycolytic flux through sensing of an intracellular metabolite, acetyl phosphate, controls the expression of two key enzymes in lycopene synthesis in response to flux dynamics. This intracellular control loop significantly enhanced lycopene production while reducing the negative impact caused by metabolic imbalance. Although we demonstrated this strategy for metabolite production, it can be extended into other fields where gene expression must be closely controlled by intracellular physiology, such as gene therapy.

3-Deoxy-7-Phosphoheptulonate Synthase↗
PubMed2000

oxLDL specifically impairs endothelium-dependent, NO-mediated dilation of coronary arterioles.

Our previous studies implicated that oxidized low-density lipoprotein (oxLDL), a putative atherogenic agent, impairs endothelium-dependent, nitric oxide (NO)-mediated dilation of isolated coronary arterioles to pharmacological agonists. However, it is not known whether oxLDL specifically affects NO-mediated dilation or generally impairs endothelium-dependent function, including the release of hyperpolarizing factors. In this regard, we investigated the dilation of isolated porcine coronary arterioles (50- to 100-microm luminal diameter) in response to the activation of various endothelium-dependent pathways before and after intraluminal incubation of the vessels with oxLDL (0.5 mg protein/ml for 60 min). In the absence of oxLDL, all vessels developed basal tone and dilated in response to the activation of NO synthase (by flow and adenosine), cyclooxygenase (by arachidonic acid), cytochrome P-450 monooxygenase (by bradykinin), and endothelial membrane hyperpolarization (by sucrose-induced hyperosmolarity). Incubation of the vessels with oxLDL for 60 min did not alter basal tone but did inhibit the vasodilatory responses to increased flow and adenosine in a manner similar to that of the NO synthase inhibitor N(G)-nitro-L-arginine methyl ester. Vasodilations in response to flow and adenosine were not affected by intraluminal incubation of the vessels with either a vehicle solution or the native LDL (0.5 mg protein/ml, 60 min). In contrast with the NO-mediated response, hyperosmotic vasodilation mediated by endothelial hyperpolarization was not affected by oxLDL. Endothelium-dependent dilations to the cyclooxygenase activator arachidonic acid and to the cytochrome P-450 monooxygenase activator bradykinin and endothelium-independent vasodilation to sodium nitroprusside were also not altered by oxLDL. Collectively, these results indicate that oxLDL has a selective effect on endothelium-dependent dilation with specific impairment of the NO-mediated response, whereas cyclooxygenase and cytochrome P-450 monooxygenase-mediated dilations are spared from this inhibitory effect. In addition, oxLDL does not appear to affect vasodilation mediated by hyperpolarization of the endothelium.

Adenosine↗
PubMed1999

Intravascular flow decreases erythrocyte consumption of nitric oxide.

Nitric oxide (NO) produced by the endothelium diffuses both into the lumen and to the smooth muscle cells according to the concentration gradient in each direction. The extremely high reaction rate between NO and hemoglobin (Hb), k(Hb)= 3-5 x 10(7) M(-1).s(-1), suggests that most of the NO produced would be consumed by Hb in the red blood cells (RBCs), which then would block the biological effect of NO. Therefore, specific mechanisms must exist under physiological conditions to reduce the NO consumption by RBCs, in which the Hb concentration is very high (24 mM heme). By using isolated microvessels as a bioassay, here we show that physiological concentrations of RBCs in the presence of intravascular flow does not inhibit NO-mediated vessel dilation, suggesting that RBCs under this condition are not an NO scavenger. On the other hand, RBCs (50% hematocrit) without intravascular flow reduce NO-mediated dilation to serotonin by 30%. In contrast, free Hb (10 microM) completely inhibits NO-mediated dilation with or without intravascular flow. The effect of flow on NO consumption by RBCs may be attributed to the formation of an RBC-free zone near the vessel wall, which is caused by hydrodynamic forces on particles. Intravascular flow does not affect the reaction rate between NO and free Hb in the lumen, because the latter forms a homogeneous solution and is not subject to the hydrodynamic separation. However, intravascular flow only partially contributes to the reduced consumption of NO by RBCs, because without the flow, the NO consumption by RBCs is already about 3 orders of magnitude slower than free Hb.

Animals↗
PubMed1999

Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic.

Modeling of metabolic pathway dynamics requires detailed kinetic equations at the enzyme level. In particular, the kinetic equations must account for metabolite effectors that contribute significantly to the pathway regulation in vivo. Unfortunately, most kinetic rate laws available in the literature do not consider all the effectors simultaneously, and much kinetic information exists in a qualitative or semiquantitative form. In this article, we present a strategy to incorporate such information into the kinetic equation. This strategy uses fuzzy logic-based factors to modify algebraic rate laws that account for partial kinetic characteristics. The parameters introduced by the fuzzy factors are then optimized by use of a hybrid of simplex and genetic algorithms. The resulting model provides a flexible form that can simulate various kinetic behaviors. Such kinetic models are suitable for pathway modeling without complete enzyme mechanisms. Three enzymes in Escherichia coli central metabolism are used as examples: phosphoenolpyruvate carboxylase; phosphoenolpyruvate carboxykinase; and pyruvate kinase I. Results show that, with fuzzy logic-augmented models, the kinetic data can be much better described. In particular, complex behavior, such as allosteric inhibition, can be captured using fuzzy rules. The resulting models, even though they do not provide additional physical meaning in enzyme mechanisms, allow the model to incorporate semiquantitative information in metabolic pathway models.

Bacterial Proteins↗