Flux balance analysis for ethylene formation in genetically engineered Saccharomyces cerevisiae.

Biosynthesis of ethylene (ethene) is mainly performed by plants and some bacteria and fungi, via two distinct metabolic routes. Plants use two steps, starting with S-adenosylmethionine, while the ethylene-forming microbes perform an oxygen dependent reaction using 2-oxoglutarate and arginine. Introduction of these systems into Saccharomyces cerevisiae was studied in silico. The reactions were added to a metabolic network of yeast and flux over the two networks was optimised for maximal ethylene formation. The maximal ethylene yields obtained for the two systems were similar in the range of 7-8 mol ethylene/10 mol glucose. The microbial metabolic network was used for testing different strategies to increase the ethylene formation. It was suggested that supplementation of exogenous proline, using a solely NAD-coupled glutamate dehydrogenase, and using glutamate as the nitrogen source, could increase the ethylene formation. Comparison of these in silico results with published experimental data for yeast expressing the microbial system confirmed an increased ethylene formation when changing nitrogen source from ammonium to glutamate. The theoretical analysis methods indicated a much higher maximal yield per glucose for ethylene than was experimentally observed. However, such high ethylene yields could only be obtained with a concomitant very high respiration (per glucose). Accordingly, when ethylene production was optimised under the additional constraint of restricted respiratory capacity (i.e. limited to experimentally measured values) the theoretical maximal ethylene yield was much lower at 0.2/10 mol glucose, and closer to the experimentally observed values.

Ethylene production by metabolic engineering of the yeast Saccharomyces cerevisiae.

The non-ethylene producing yeast, Saccharomyces cerevisiae, was transformed into an ethylene producer by introducing the ethylene forming enzyme from the plant pathogenic bacterium Pseudomonas syringae. Cultivation of the metabolically engineered strain was performed in well-controlled bioreactors as aerobic batch cultures with an on-line monitoring of ethylene production. The highest productivity was obtained during the respiro-fermentative growth on glucose but there was also a significant rate of formation during the subsequent phase of ethanol respiration. Furthermore, investigations were performed whether substitution of the original nitrogen source, NH(4)(+), for glutamate could improve productivity and yield of ethylene even more. The rationale being that one of the substrates for the enzyme is 2-oxoglutarate and this compound can be formed from glutamate in a single reaction. Indeed, there was a substantial improvement in the rate of production and the final yield of ethylene was almost three times higher when NH(4)(+) was replaced by glutamate.

Engineering of a novel Saccharomyces cerevisiae wine strain with a respiratory phenotype at high external glucose concentrations.

The recently described respiratory strain Saccharomyces cerevisiae KOY.TM6*P is, to our knowledge, the only reported strain of S. cerevisiae which completely redirects the flux of glucose from ethanol fermentation to respiration, even at high external glucose concentrations (27). In the KOY.TM6*P strain, portions of the genes encoding the predominant hexose transporter proteins, Hxt1 and Hxt7, were fused within the regions encoding transmembrane (TM) domain 6. The resulting chimeric gene, TM6*, encoded a chimera composed of the amino-terminal half of Hxt1 and the carboxy-terminal half of Hxt7. It was subsequently integrated into the genome of an hxt null strain. In this study, we have demonstrated the transferability of this respiratory phenotype to the V5 hxt1-7Delta strain, a derivative of a strain used in enology. We also show by using this mutant that it is not necessary to transform a complete hxt null strain with the TM6* construct to obtain a non-ethanol-producing phenotype. The resulting V5.TM6*P strain, obtained by transformation of the V5 hxt1-7Delta strain with the TM6* chimeric gene, produced only minor amounts of ethanol when cultured on external glucose concentrations as high as 5%. Despite the fact that glucose flux was reduced to 30% in the V5.TM6*P strain compared with that of its parental strain, the V5.TM6*P strain produced biomass at a specific rate as high as 85% that of the V5 wild-type strain. Even more relevant for the potential use of such a strain for the production of heterologous proteins and also of low-alcohol beverages is the observation that the biomass yield increased 50% with the mutant compared to its parental strain.

A systems evaluation on the effectiveness of a catalyst retrofit program in China.

A low-cost, rare-earth oxide (REO) catalyst has been recommended as part of China's retrofit program for Chinese carbureted vehicles. This study evaluated: (1) the emission reduction efficiency of the REO catalyst during chassis dynamometer testing on the FTP cycle; (2) the effect that fuel properties had on tailpipe emissions and catalyst efficiency; (3) the importance of vehicle premaintenance as part of a retrofit protocol; and (4) the emission reductions obtained following implementation of the program. Results also show that current in-use Chinese noncatalyst, carbureted vehicles operate excessively rich, resulting in extremely high emissions of CO, gaseous toxic compounds, and other non-methane hydrocarbon species (NMHC). Preretrofit maintenance alone has the potential to reduce these emissions by approximately 50%. Dynamometer emission tests showed emissions reductions of >95% for hydrocarbons, CO, and gaseous toxics after retrofit of the REO catalyst. In particular, the relative unit health risk associated with the decrease in emissions of airborne toxic compounds using unleaded Chinese fuel was reduced from 6.33 to 0.30. (Use of low-sulfur California Phase II gasoline rather than current in-use Chinese fuel reduced emissions further.) Following implementation of the program, a follow-up study showed that in-use emissions benefits were considerably less than anticipated, primarily because of poor quality control at the retrofit service centers, a less aggressive preretrofit maintenance procedure, and unauthorized modification to the recommended retrofit control system. Overall results indicate that a carefully controlled retrofit program using REO catalyst technology can reduce emissions significantly. However, well-defined implementation guidelines, and strict adherence to these guidelines are needed to achieve maximum benefits.

Time-resolved characterization of diesel particulate emissions. 2. Instruments for elemental and organic carbon measurements.

The measurement of elemental carbon (EC) and organic carbon (OC) mass for particles emitted by diesel vehicles is currently accomplished using particle collection on filters, followed by analysis using the thermal/optical reflectance carbon analysis method (TOR) or one of its variations. Such filter methods limit time resolution to a minimum of several minutes, making it impossible to study emissions during transient operating conditions. Testing of five different measurement methods has demonstrated that fast response measurement of diesel exhaust particulate EC and OC concentrations, consistent with TOR filter measurements, is feasible using existing technology. EC mass concentrations are best measured through determination of particulate light absorption with a photoacoustic instrument or determination of light extinction with a smoke meter. The photoacoustic instrument has the better dynamic range and sensitivity, whereas the smoke meter is a simpler instrument. Fast response OC measurements cannot be made with any single instrument tested. However, a combination of real time weighing as implemented in the tapered element oscillating microbalance with the photoacoustic instrument has been shown to be capable of determining OC concentrations with good time response. The addition of a nephelometer to the OC measurement could potentially improve time resolution, freedom from interferences, and sensitivity.

Time resolved characterization of diesel particulate emissions. 1. Instruments for particle mass measurements.

The measurement of diesel vehicle exhaust particulate mass is currently accomplished using filter collection methods according to the Code of Federal Regulations (CFR). Such filter methods limit time resolution to a minimum of several minutes, making it impossible to study emissions during transient operating conditions. Extensive testing of five different measurement methods has demonstrated that fast response measurements of diesel exhaust particulate mass concentrations, consistent with CFR filter measurements, are feasible using existing technology. The measurement principles of choice are the real time weighing of exhaust samples as implemented in the tapered element oscillating microbalance (TEOM) and the measurement of light scattering from exhaust particles as implemented in the DustTrak nephelometer. Each of these two instruments has distinctive strengths. The TEOM excels in the area of constant calibration, independent of vehicle. For the DustTrak, this calibration varies by vehicle. On the other hand, the DustTrak has an excellent signal-to-noise ratio, freedom from interference due to other exhaust sample properties, good time resolution, and simplicity. The strengths of the two measurement methods are complimentary, so an obvious suggestion is to integrate them. The nephelometer would obtain a fast response signal, with near real time calibration provided by the microbalance.

Adhesion of type 1-fimbriated Escherichia coli to abiotic surfaces leads to altered composition of outer membrane proteins.

Phenotypic differences between planktonic bacteria and those attached to abiotic surfaces exist, but the mechanisms involved in the adhesion response of bacteria are not well understood. By the use of two-dimensional (2D) polyacrylamide gel electrophoresis, we have demonstrated that attachment of Escherichia coli to abiotic surfaces leads to alteration in the composition of outer membrane proteins. A major decrease in the abundance of resolved proteins was observed during adhesion of type 1-fimbriated E. coli strains, which was at least partly caused by proteolysis. Moreover, a study of fimbriated and nonfimbriated mutants revealed that these changes were due mainly to type 1 fimbria-mediated surface contact and that only a few changes occurred in the outer membranes of nonfimbriated mutant strains. Protein synthesis and proteolytic degradation were involved to different extents in adhesion of fimbriated and nonfimbriated cells. While protein synthesis appeared to affect adhesion of only the nonfimbriated strain, proteolytic activity mostly seemed to contribute to adhesion of the fimbriated strain. Using matrix-assisted laser desorption ionization-time of flight mass spectrometry, six of the proteins resolved by 2D analysis were identified as BtuB, EF-Tu, OmpA, OmpX, Slp, and TolC. While the first two proteins were unaffected by adhesion, the levels of the last four were moderately to strongly reduced. Based on the present results, it may be suggested that physical interactions between type 1 fimbriae and the surface are part of a surface-sensing mechanism in which protein turnover may contribute to the observed change in composition of outer membrane proteins. This change alters the surface characteristics of the cell envelope and may thus influence adhesion.

Nucleocytoplasmic distribution of budding yeast protein kinase A regulatory subunit Bcy1 requires Zds1 and is regulated by Yak1-dependent phosphorylation of its targeting domain.

In Saccharomyces cerevisiae the subcellular distribution of Bcy1 is carbon source dependent. In glucose-grown cells, Bcy1 is almost exclusively nuclear, while it appears more evenly distributed between nucleus and cytoplasm in carbon source-derepressed cells. Here we show that phosphorylation of its N-terminal domain directs Bcy1 to the cytoplasm. Biochemical fractionation revealed that the cytoplasmic fraction contains mostly phosphorylated Bcy1, whereas unmodified Bcy1 is predominantly present in the nuclear fraction. Site-directed mutagenesis of two clusters (I and II) of serines near the N terminus to alanine resulted in an enhanced nuclear accumulation of Bcy1 in ethanol-grown cells. In contrast, substitutions to Asp led to a dramatic increase of cytoplasmic localization in glucose-grown cells. Bcy1 modification was found to be dependent on Yak1 kinase and, consequently, in ethanol-grown yak1 cells the Bcy1 remained nuclear. A two-hybrid screen aimed to isolate genes encoding proteins that interact with the Bcy1 N-terminal domain identified Zds1. In ethanol-grown zds1 cells, cytoplasmic localization of Bcy1 was largely absent, while overexpression of ZDS1 led to increased cytoplasmic Bcy1 localization. Zds1 does not regulate Bcy1 modification since this was found to be unaffected in zds1 cells. However, in zds1 cells cluster II-mediated, but not cluster I-mediated, cytoplasmic localization of Bcy1 was found to be absent. Altogether, these results suggest that Zds1-mediated cytoplasmic localization of Bcy1 is regulated by carbon source-dependent phosphorylation of cluster II serines, while cluster I acts in a Zds1-independent manner.

Comparison of the proteomes of three yeast wild type strains: CEN.PK2, FY1679 and W303.

Yeast deletion strains created during gene function analysis projects very often show drastic phenotypic differences depending on the genetic background used. These results indicate the existence of important molecular differences between the CEN.PK2, FY1679 and W303 wild type strains. To characterise these differences we have compared the protein expression levels between CEN.PK2, FY1679 and W303 strains using twodimensional gel electrophoresis and identified selected proteins by mass spectrometric analysis. We have found that FY1679 and W303 strains are more similar to each other than to the CEN.PK2 strain. This study identifies 62 proteins that are differentially expressed between the strains and provides a valuable source of data for the interpretation of yeast mutant phenotypes observed in CEN.PK2, FY1679 and W303 strains.

Fermentative capacity after cold storage of baker's yeast is dependent on the initial physiological state but not correlated to the levels of glycolytic enzymes.

Growth and starvation of baker's yeast was monitored by on-line microcalorimetry and cells originating from four different physiological states were stored at low temperature (4 degrees C) for up to 26 days. The different physiological states were designated F (respiro-Fermentative phase of growth), R (initial Respiratory phase of growth), -N (non-growing state because of Nitrogen depletion), and -NC (non-growing state because of both Nitrogen and Carbon depletion). The cells were tested before and after cold storage for their fermentative capacity, and characterised by 2D gel analysis (and subsequent quantitative silver staining and image analysis with software PDQUEST) for their levels of six enzymes of the glycolytic pathway (hexokinase 2 (Hxk2p), fructose bisphosphate aldolase (Fba1p), glyceraldehyde-3-phosphate dehydrogenase (Tdh3p), enolase A (Enolp), enolase B (Eno2p), and triose phosphate isomerase (Tpi1p)) and two enzymes of the fermentative branch (pyruvate decarboxylase (Pdc1p) and alcohol dehydrogenase (Adh1p)). The enzymes Hxk2p, Tdh3p, Eno2p, Pdc1p and Adh1p were down-regulated by 25-80% during the transition between the F and R states. During the transition to non-growing states (-N and -NC states), the levels of Hxk2p, Tdh3p and Eno2p were further reduced. However, after cold storage, the glycolytic and fermentative enzymes of the different physiological states were expressed to the same extent. In contrast, the fermentative capacity differed between the states; the R-state cells were superior compared to cells from the other states tested and preserved more than 50% of their initial fermentative capacity (6 mmol ethanol per gram dry weight and hour). Our data therefore clearly demonstrate that persistence of fermentative capacity during total starvation at low temperature after as long as 1 month is strongly dependent on the physiological state from which the cells originate. However, the level of expression of the glycolytic enzymes could not explain the difference in fermentative capacity of the different physiological states after cold storage.

An open-label study of a functional opioid kappa antagonist in the treatment of opioid dependence.

Several lines of evidence, including the well-established observation that kappa opiate agonists produce dysphoria and psychotomimetic effects in humans, suggest that dysfunction of the endogenous kappa opioid system may contribute to opioid and cocaine addiction. The objective of this open-label study was to determine the effectiveness of a functional kappa antagonist as a treatment for opioid dependence. This was accomplished by combining a partial mu agonist/kappa antagonist (buprenorphine, 4 mg, sublingual) with a mu antagonist (naltrexone, 50 mg by mouth), theoretically leaving kappa antagonism as the major medication effect. Subjects were treatment-seeking heroin-dependent (as per Diagnostic and Statistical Manual of Mental Disorders, 4th ed.) men (41 +/- 7 years old; 19 +/- 8 years heroin use) eligible for methadone maintenance. After inpatient detoxification and a naloxone-challenge test to verify that they were not physically dependent on opioids, subjects received naltrexone. Starting on the fourth day, patients also received liquid buprenorphine. All patients received medication at the clinic 6 days per week and a full program of psychosocial treatment. The major endpoints of the study were: pupil diameter to determine if the mu agonist effects of buprenorphine were blocked by naltrexone, urine toxicology, and retention in treatment. Five patients (33%) completed the 3-month study. Four were abstinent from opioids and cocaine for the entire study, and one was abstinent from opioids and cocaine for the last 9 weeks. Six subjects dropped out due to either minor side effects or disliking the sensation of sublingual buprenorphine. There were no significant changes in pupillary diameter. The positive response to treatment exceeds that expected from naltrexone alone (90% dropout). These promising results suggest that controlled studies of this medication combination should be conducted.

The level of cAMP-dependent protein kinase A activity strongly affects osmotolerance and osmo-instigated gene expression changes in Saccharomyces cerevisiae.

The influence of cAMP-dependent protein kinase (PKA) on protein expression during exponential growth under osmotic stress was studied by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). The responses of isogenic strains (tpk2Deltatpk3Delta) with either constitutively low (tpk1(w1)), regulated (TPK1) or constitutively high (TPK1bcy1Delta) PKA activity were compared. The activity of cAMP-dependent protein kinase (PKA) was shown to be a major determinant of osmotic shock tolerance. Proteins with increased expression during growth under sodium chloride stress could be grouped into three classes with respect to PKA activity, with the glycerol metabolic proteins GPD1, GPP2 and DAK1 standing out as independent of PKA. The other osmotically induced proteins displayed a variable dependence on PKA activity; fully PKA-dependent genes were TPS1 and GCY1, partly PKA-dependent genes were ENO1, TDH1, ALD3 and CTT1. The proteins repressed by osmotic stress also fell into distinct classes of PKA-dependency. Ymr116c was PKA-independent, while Pgi1p, Sam1p, Gdh1p and Vma1p were fully PKA-dependent. Hxk2p, Pdc1p, Ssb1p, Met6p, Atp2p and Hsp60p displayed a partially PKA-dependent repression. The promotors of all induced PKA-dependent genes have STRE sites in their promotors suggestive of a mechanism acting via Msn2/4p. The mechanisms governing the expression of the other classes are unknown. From the protein expression data we conclude that a low PKA activity causes a protein expression resembling that of osmotically stressed cells, and furthermore makes cells tolerant to this type of stress.

Identification and specificities of N-terminal acetyltransferases from Saccharomyces cerevisiae.

N-terminal acetylation can occur cotranslationally on the initiator methionine residue or on the penultimate residue if the methionine is cleaved. We investigated the three N-terminal acetyltransferases (NATs), Ard1p/Nat1p, Nat3p and Mak3p. Ard1p and Mak3p are significantly related to each other by amino acid sequence, as is Nat3p, which was uncovered in this study using programming alignment procedures. Mutants deleted in any one of these NAT genes were viable, but some exhibited diminished mating efficiency and reduced growth at 37 degrees C, and on glycerol and NaCl-containing media. The three NATs had the following substrate specificities as determined in vivo by examining acetylation of 14 altered forms of iso-1-cytochrome c and 55 abundant normal proteins in each of the deleted strains: Ard1p/Nat1p, subclasses with Ser-, Ala-, Gly- and Thr-termini; Nat3p, Met-Glu- and Met-Asp- and a subclass of Met-Asn-termini; and Mak3p subclasses with Met-Ile- and Met-Leu-termini. In addition, a special subclass of substrates with Ser-Glu- Phe-, Ala-Glu-Phe- and Gly-Glu-Phe-termini required all three NATs for acetylation.

Thiamine repression and pyruvate decarboxylase autoregulation independently control the expression of the Saccharomyces cerevisiae PDC5 gene.

The Saccharomyces cerevisiae gene PDC5 encodes the minor isoform of pyruvate decarboxylase (Pdc). In this work we show that expression of PDC5 but not that of PDC1, which encodes the major isoform, is repressed by thiamine. Hence, under thiamine limitation both PDC1 and PDC5 are expressed. PDC5 also becomes strongly expressed in a pdc1delta mutant. Two-dimensional gel electrophoresis of whole protein extracts shows that thiamine limitation stimulates the production of THI gene products and of Pdc5p. Deletion of PDC1 only stimulates production of Pdc5p. We conclude that the stimulation of PDC5 expression in a pdc1delta mutant is not due to a response to thiamine limitation.

Quantitative aspects of the use of bacterial chloramphenicol acetyltransferase as a reporter system in the yeast Saccharomyces cerevisiae.

The quantitative aspects of the use of the reporter system chloramphenicol acetyltransferase (CAT) has been evaluated in the yeast Saccharomyces cerevisiae. It was found that the CAT activity measured with a radiosotopic fluor diffusion assay was strongly dependent on the amount of yeast extract applied, both when CAT was expressed endogenously and when a purified Escherichia coli enzyme was investigated. Desalting the yeast extract by gel filtration partly eliminated the problem, indicating that some low-molecular-weight compound was involved in the phenomenon. However, the extract still exhibited stability problems on ice. An immunological CAT assay was tested and found to yield satisfactory quantitative result.

The personal experience of pregnancy for African-American women.

This study describes the personal experiences of pregnancy for African-American women. Data were obtained from two group interviews with four African-American nurse-midwives who had experienced pregnancy and had extensive professional experience in the provision of health care services to pregnant African Americans. Three major themes were constructed from the interview narratives. The first concerned the experience of pregnancy as a transition experience from childhood to adulthood and from womanhood to motherhood, involving heightened senses of maturity, self-esteem, and intimacy. The second identified stresses experienced by African-American women, including the lack of material resources and emotional support. The last theme concerned the provision of effective support in pregnancy. The significance of interpersonal relationships with the pregnant women's mothers, other significant women, and their partners was described. Implications for practice included suggestions for the provision of effective emotional support from health care professionals such as attentive listening and the elimination of environmental factors that communicate lowered personal value.

Teaching, research, and service: striking the balance in doctoral education.

The concept of balance across the multiple role expectations of faculty is a relative term that should be understood in the context of the mission of a particular institution and as it relates to the external environment. Various metaphors or visual images of balance carry symbolic meanings. During this dynamic period in higher education, images of balance that suggest that creativity and the capacity for change are preferable to static forms. Models for defining balance are presented that include two levels of analysis (the individual faculty member and the institutional level) and two temporal variations (continuous balance versus balance over a period of time). Strategies identified by faculty that enhance faculty productivity included both individual and institutional characteristics. Formal faculty development activities are also described. Those aimed at the individual level include orientation, mentoring, peer expertise, and use of sabbaticals or leaves. Institutional approaches to faculty development relate to the reward structure and recognition systems and use workshops and centers for providing faculty development. Based on changes occurring in the health care system and in higher education, implications for changes in faculty roles in the future are discussed.

Amino acid uptake is strongly affected during exponential growth of Saccharomyces cerevisiae in 0.7 M NaCl medium.

Labelling of Saccharomyces cerevisiae grown in 0.7 M NaCl with 35S-methionine revealed a 5-6 fold lowering of the methionine incorporation into protein, which could not be attributed solely to the approximately 50% longer generation time of cells grown in 0.7 M NaCl. Subsequent studies of the high affinity methionine uptake system showed a strongly reduced uptake of methionine during growth in 0.7 M NaCl medium. This reduced uptake was shown to be strain-independent and caused mainly by an approximately 20-fold lowered maximum velocity (Vmax) of the transport system, while the substrate affinity (Km) displayed only a minor change. A salt-instigated reduction of uptake was furthermore demonstrated for the leucine and histidine high affinity uptake systems and also for a mixture of 15 different amino acids. We therefore suggest that the reduced amino acid uptake is a general phenomenon observed in salt-grown cells.

Naltrexone as an adjunctive treatment for older patients with alcohol dependence.

The authors examined the efficacy of naltrexone as an adjunctive treatment for alcohol dependence in older adults. Forty-four veterans over 50 years of age were enrolled in a 12-week, double-blind, placebo-controlled efficacy study of naltrexone (the equivalent of 50 mg per day). There were no differences in the frequency of any self-reported adverse effects or in liver enzyme values between the placebo- and naltrexone-treated groups. There were no differences between the treatment groups in the number of subjects remaining abstinent or in the number of subjects who relapsed. However, all placebo-treated subjects relapsed after sampling alcohol, whereas only three of six naltrexone-treated subjects met relapse criteria after alcohol exposure (P = 0.024). The authors conclude that naltrexone was well tolerated and efficacious in preventing relapse in subjects who drank.

Identification of two-dimensional gel electrophoresis resolved yeast proteins by matrix-assisted laser desorption ionization mass spectrometry.

Protein extract from yeast cells growing exponentially in saline medium was separated by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), with the separation in the first dimension on a wide range immobilized pH (3-10) gradient. From one preparative 2-D gel a number of previously identified proteins were used as test material for our initial matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) efforts on large scale rapid protein spot identification. Sample preparation via in-gel trypsin digestion was slightly modified to be compatible to MS analysis, and via this modified procedure MS generated peptide mass profiles could, in most cases with good precision, identify the protein in question. Preferential ionization was tested on a yeast aldehyde dehydrogenase (ALD7), and it was shown that the ionization of some peptides was clearly suppressed by the presence of others. Roughly 50% of the observed peptide masses was found by the search routines in the database, and the mass measurement accuracy of the peptides was within 0.5 Da. Silver-stained gels could be used with good results for the generation of peptides to be analyzed by MALDI-MS. For one of the 2-D resolved proteins, glycerol 3-phosphatase (GPP1), the post-source decay (PSD) spectrum proved crucial in identification.