MPS: An artificially intelligent software system for the analysis and synthesis of metabolic pathways

The concepts of artificial intelligence have been applied for the development of a software system for metabolic pathway synthesis (MPS). An easily expandable data base system for storing enzyme and substance descriptions is used by a search algorithm for the identification of possible ways to interconvert carbon-carrying metabolites. A versatile screening capability permits the user to identify all pathways which contain or exclude any combination of enzymes, substrates, and/or products. Information provided by MPS can be used to predict on a qualitative basis the effects of adding or deleting enzymatic activities to or from the cellular environment, to classify pathways with respect to cellular objectives, and to extract information about metabolic regulation. MPS can be used subsequently to aid the identification of appropriate genotypes or genetic modifications that will redirect metabolism towards amplified production of desirable bioproducts. Two examples illustrating the capabilities of MPS are presented. In the first example, which considers the conversion of glucose 6-phosphate to pyruvate, MPS synthesized the classical catabolic pathways (EMP, pentose phosphate and ED) along with possible variations. A route for the biosynthesis of L-alanine that does not incorporate the enzyme alanine aminotransferase was revealed by MPS during synthesis of alternative pathways which produce L-alanine from pyruvate.

Communication to the editor. Application of the cross-regulation system as a metabolic switch

The ability to switch metabolic flow from one pathway to another at a desired point in a bioprocess expands the horizons of metabolic engineering. Such an externally inducible switch can be realized by embedding synthetic operons behind tow corss-regulated promoters. This results in coordinated cessation of transcription of one operon while transcription of a second operon is simultaneously activated. The ability to effect such coordinated and inverse control of transcription of two operons has been illustrated experimentally using a model construct containing two different reporter genes, Vitreoscilla hemoglobin (VHb) and chloramphenicol acetyltransferase (CAT), fused to lambdaP(L) and tac promoters, respectively, along with corresponding repressor genes in a cross-regulation configuration. Only VHb production was observed preinduction, and postinduction only CAT was produced. The framework presented here and its obvious extensions can be used with different combinations of promoter systems and synthetic operon constructs to achieve complicated metabolic flux regulation in diverse host. (c) 1994 John Wiley & Sons, Inc.

Improvement of Escherichia coli microaerobic oxygen metabolism by Vitreoscilla hemoglobin: New insights from NAD(P)H fluorescence and culture redox potential

On-line NAD(P)H fluorescence and culture redox potential (CRP) measurements were utilized to investigate the role of Vitreoscilla hemoglobin (VHb) in perturbing oxygen metabolism of microaerobic Escherichia coli Batch cultures of a VHb-synthesizing E. coli strain and the iso-genic control under fully aerated conditions were subject to several high/low oxygen transitions, and the NAD(P)H fluorescence and CRP were monitored during these passages. The presence of VHb decreased the rate of net NAD(P)H generation by 2.4-fold under diminishing oxygen tension. In the absence of aeration, the strain producing VHb maintained a steady NAD(P)H level 1.8-fold less than that of the control, indicating that the presence of VHb keeps E. coli in a more oxidized state under oxygen-limited conditions. Estimated from CRP, the oxygen uptake rates near anoxia were 25% higher for cells with VHb than those without. These results suggest that VHb-expressing cells have a higher microaerobic electron transport chain turnover rate. To examine how NAD(P)H utilization of VHb-expressing cells responds to rapidly changing oxygen tension, which is common in large-scale fermentations, we pulsed air intermittently into a cell suspension and recorded the fluorescence response to the imposed dissolved oxygen (DO) fluctuation. Relative to the control, cells containing VHb had a sluggish fluorescence response to sudden changes of oxygen tension, suggesting that VHb buffers intracellular redox perturbations caused by extracellular DO fluctuations.(c) John Wiley & Sons, Inc.

A methodology for calibrating wavelength dependent spectral resolution for crystal spectrometers

High quality absorption spectroscopy measurements were recently achieved at the Sandia National Laboratories Z facility in the soft x-ray range. Detailed spectral resolution knowledge is a key requirement for their interpretation. We present a methodology for measuring the wavelength dependent crystal spectral resolution, with a particular focus on the 7-17 Å range. We apply this procedure to the case of 1st order resolution of a potassium acid phthalate (KAP) convex crystal spectrometer. One calibration issue is that inferring the crystal resolution requires that the x-ray source emission feature widths and spectral profiles are known. To this aim, we resolve Manson x-ray source Si, Al, and Mg Kα line profiles using a KAP crystal spectrometer in 2nd order to achieve relatively high resolution. This information is exploited to measure 1st order KAP resolving powers λ∕Δλ∼1100-1300 in the 7-10 Å wavelength range.

Pinned, optically aligned diagnostic dock for use on the Z facility

The pinned optically aligned diagnostic dock (PODD) is a multi-configuration diagnostic platform designed to measure x-ray emission on the Z facility. The PODD houses two plasma emission acquisition (PEA) systems, which are aligned with a set of precision machined pins. The PEA systems are modular, allowing a single diagnostic housing to support several different diagnostics. The PEA configurations fielded to date include both time-resolved and time-integrated, 1D spatially resolving, elliptical crystal spectrometers, and time-integrated, 1D spatially resolving, convex crystal spectrometers. Additional proposed configurations include time-resolved, monochromatic mirrored pinhole imagers and arrays of filtered x-ray diodes, diamond photo-conducting diode detectors, and bolometers. The versatility of the PODD system will allow the diagnostic configuration of the Z facility to be changed without significantly adding to the turn-around time of the machine. Additionally, the PODD has been designed to allow instrument setup to be completed entirely off-line, leaving only a refined alignment process to be performed just prior to a shot, which is a significant improvement over the instrument the PODD replaces. Example data collected with the PODD are presented.

Investigation of iron opacity experiment plasma gradients with synthetic data analyses

Experiments have been performed at Sandia National Laboratories Z-facility to validate iron opacity models relevant to the solar convection/radiation zone boundary. Sample conditions were measured by mixing Mg with the Fe and using Mg K-shell line transmission spectra, assuming that the plasma was uniform. We develop a spectral model that accounts for hypothetical gradients, and compute synthetic spectra to quantitatively evaluate the plasma gradient size that can be diagnosed. Two sample designs are investigated, assuming linear temperature and density gradients. First, Mg uniformly mixed with Fe enables temperature gradients greater than 10% to be detected. The second design uses Mg mixed into one side and Al mixed into the other side of the sample in an attempt to more accurately infer the sample gradient. Both temperature and density gradients as small as a few percent can be detected with this design. Experiments have successfully recorded spectra with the second design. In future research, the spectral model will be used to place bounds on gradients that exist in Z opacity experiments.

Prevalence of malignancy in thyroid nodules with an initial nondiagnostic result after ultrasound guided fine needle aspiration

The objective of this study was to determine the rate of malignancy in thyroid nodules with an initial nondiagnostic fine needle aspiration. From October 2001 to April 2007, biopsies were performed on 1344 thyroid nodules in our practice. Biopsies were performed on nodules using 25-27 gauge needles, ultrasound guidance and multiple passes using both suction and capillary action. We retrospectively reviewed the results of these biopsies as well as any further management of nodules that received nondiagnostic results (IRB HUM00006459). Following initial biopsy, 295/1344 (21.9%) of nodules received nondiagnostic pathologic results. Of this population, 39 nodules (13.1%) were lost to follow-up. Of the remaining 256 nodules that received a repeat FNA, surgical excision, or greater than 24 months of clinical and imaging follow-up, only five cancers were detected, representing only 2% of the population that received an initial nondiagnostic biopsy result. All of these cancers were papillary neoplasms. When rigorous, ultrasound-guided, fine needle aspiration of thyroid nodules is performed, a nondiagnostic histopathologic result should not be interpreted as suspicious for thyroid cancer. Given the low rate of malignancy in this population (2%), we suggest that clinical and imaging follow-up of these nodules, opposed to repeat sampling, is warranted.

The effectiveness and cost of single and multi-factorial cardiovascular risk factor modification to guideline targets in type 2 diabetes

AIMS

Cardiovascular disease is the main cause of morbidity and mortality in type 2 diabetes (T2DM), at huge cost to the NHS. We investigated the potential effect on population cardiovascular risk and associated costs of single and multi-factorial intervention, to target levels, in individuals with T2DM.

METHODS

Baseline population means and proportions for cardiovascular risk factors were calculated for 159 patients with T2DM from 3 general practices. Predicted 10year cardiovascular risk, and associated costs were calculated using the LIP2687 risk calculator, based on Framingham and UKPDS equations. Systolic blood pressure, HbA(1C), total cholesterol and HDL-cholesterol were altered to NICE and SIGN target levels and the model run again. The difference in outcomes was observed.

RESULTS

45%, 76% and 38% of patients met NICE targets for cholesterol, systolic blood pressure and HbA1c, respectively. As expected, comparing the two guidelines, fewer patients met the 'stricter' targets (P=0.0001). Treatment-to-target produced no significant difference in cardiovascular risk or costs, although greater reductions in outcomes were seen with multi-factorial intervention.

CONCLUSION

This small study suggests that intervention in only those patients with the highest cardiovascular risk brings little reduction in population cardiovascular risk and associated health costs. Multi-factorial intervention in all patients with T2DM, regardless of baseline values, is likely to bring greater reductions. This raises the question as to whether the current emphasis on treatment to target should be modified to encourage multi-factorial intervention in all patients with T2DM, even those with baseline values below target levels.

Imaging radiation-induced normal tissue injury

Technological developments in radiation therapy and other cancer therapies have led to a progressive increase in five-year survival rates over the last few decades. Although acute effects have been largely minimized by both technical advances and medical interventions, late effects remain a concern. Indeed, the need to identify those individuals who will develop radiation-induced late effects, and to develop interventions to prevent or ameliorate these late effects is a critical area of radiobiology research. In the last two decades, preclinical studies have clearly established that late radiation injury can be prevented/ameliorated by pharmacological therapies aimed at modulating the cascade of events leading to the clinical expression of radiation-induced late effects. These insights have been accompanied by significant technological advances in imaging that are moving radiation oncology and normal tissue radiobiology from disciplines driven by anatomy and macrostructure to ones in which important quantitative functional, microstructural, and metabolic data can be noninvasively and serially determined. In the current article, we review use of positron emission tomography (PET), single photon emission tomography (SPECT), magnetic resonance (MR) imaging and MR spectroscopy to generate pathophysiological and functional data in the central nervous system, lung, and heart that offer the promise of, (1) identifying individuals who are at risk of developing radiation-induced late effects, and (2) monitoring the efficacy of interventions to prevent/ameliorate them.

Doppler measurement of implosion velocity in fast Z-pinch x-ray sources

The observation of Doppler splitting in K-shell x-ray lines emitted from optically thin dopants is used to infer implosion velocities of up to 70 cm/μs in wire-array and gas-puff Z pinches at drive currents of 15-20 MA. These data can benchmark numerical implosion models, which produce reasonable agreement with the measured velocity in the emitting region. Doppler splitting is obscured in lines with strong opacity, but red-shifted absorption produced by the cooler halo of material backlit by the hot core assembling on axis can be used to diagnose velocity in the trailing mass.

Apprenticeships ease the transition to independent call: an evaluation of anxiety and confidence among junior radiology residents

RATIONALE AND OBJECTIVES

The aims of this study were to quantify resident anxiety when beginning independent call and to assess whether an apprenticeship experience (buddy call) can lessen anxiety and improve confidence.

MATERIALS AND METHODS

A prospective cohort comparison of two groups of radiology residents beginning independent call, one of which was provided with a buddy call experience, was performed. Anxiety and confidence were assessed using the Endler Multidimensional Anxiety Scales-State (EMAS-S), with total score, autonomic emotional, and cognitive worry components, and a five-point, Likert-type scale, respectively. Both groups were asked about the perceived value of a buddy call experience.

RESULTS

EMAS-S scores improved significantly over 5 days of call in both groups (control, n = 10, P = .0005; buddy call, n = 9, P = .0001), and image interpretation confidence correspondingly increased (control, P = .0004; buddy call, P = .003). Compared to the control group, autonomic emotional scores were significantly lower in the buddy call group on the first day of independent call (P = .040), and cognitive worry and total EMAS-S scores were significantly lower on day 5 (both P values = .03). Buddy call was independently associated with improved autonomic emotional and film interpretation confidence scores (both P values = .02). All members of the buddy call group indicated that the experience was very helpful in preparing for call.

CONCLUSIONS

Beginning independent call is associated with high anxiety, and buddy call reduces that anxiety, beyond the effect of time alone. Residents who participated in buddy call found it helpful in preparing for independent call. These findings support the use of buddy call and tiered call structures as means to introduce junior residents to independent call.

pQuattro vectors allow one-step multigene metabolic engineering and auto-selection of quattrocistronic artificial mammalian operons

Based on internal ribosomal entry sites (IRES) of picornaviral origin we constructed a novel family of mammalian expression vectors. pQuattro vectors contain quattrocistronic artificial eukaryotic operons which link, in a single transcript, the simultaneous and coordinated as well as adjustable expression of up to three independent genes of interest to a terminal neomycin (neo) resistance marker. Due to the strict genetic linkage of the transgenes and the terminal selection marker, this genetic configuration enables, by the selection on neomycin, multigene metabolic engineering of mammalian cells in a single step (one-step metabolic engineering). Furthermore, selection on the terminal cistron of multicistronic expression units enforces cocistronic expression of all upstream encoded genes and maximises genetic integrity of the eukaryotic operon in stable mammalian cell lines, since clones harbouring damaged multicistronic expression units become neomycin-sensitive and are automatically counterselected (auto-selection). The modular set-up and the abundance of restriction sites in pQuattro vectors facilitate the movement of individual genes between multicistronic expression vectors and guarantees high compatibility with genetic elements of a wide variety of existing mammalian expression vectors.

Regulated multicistronic expression technology for mammalian metabolic engineering

Contemporary basic research is rapidly revealing increasingly complex molecular regulatory networks which are often interconnected via key signal integrators. These connections among regulatory and catalytic networks often frustrate bioengineers as promising metabolic engineering strategies are bypassed by compensatory metabolic responses or cause unexpected, undesired outcomes such as apoptosis, product protein degradation or inappropriate post- translational modification. Therefore, for metabolic engineering to achieve greater success in mammalian cell culture processes and to become important for future applications such as gene therapy and tissue engineering, this technology must be enhanced to allow simultaneous, in cases conditional, reshaping of metabolic pathways to access difficult-to-attain cell states. Recent advances in this new territory of multigene metabolic engineering are intimately linked to the development of multicistronic expression technology which allows the simultaneous, and in some cases, regulated expression of several genes in mammalian cells. Here we review recent achievements in multicistronic expression technology in view of multigene metabolic engineering.

Posterior acoustic enhancement in hepatocellular carcinoma

OBJECTIVES

The purpose of this study was to assess sonographic appearances of hepatocellular carcinoma with particular attention to posterior acoustic effects.

METHODS

We performed an Institutional Review Board-approved retrospective review of patients with hepatocellular carcinoma who had undergone sonographically guided procedures in our department between 2001 and 2010. A total of 247 masses thought to represent hepatocellular carcinoma were identified; 27 were excluded because of prior angioembolization (altering the sonographic appearance), alternate histologic diagnoses, and incomplete patient information or imaging. Ultimately, 220 masses in 185 patients (138 men and 47 women; average age, 59.1 years) constituted the study population. Preprocedure sonograms were reviewed in consensus by 3 abdominal radiologists; the liver echo texture, lesion echogenicity, and posterior acoustic effect were rated and correlated with patient data.

RESULTS

The average mass size was 3.1 cm (range, 0.7-17 cm). In total, 84.1% of the masses (n = 185) arose in abnormally echogenic/attenuating livers; 54.1% of the masses (n = 119) were predominantly hypoechoic, 23.2% (n = 51) isoechoic, and 22.7% (n = 50) hyperechoic. Target-type morphologic characteristics were noted in 41 masses. Many masses (52.7% [n = 116]) had no specific posterior acoustic effect, but nearly half (46.4%) had either mild (n = 64) or marked (n = 38) posterior acoustic enhancement. The remaining masses (0.9% [n = 2]) had posterior shadowing. Posterior acoustic enhancement was most common among hyperechoic masses (62% with posterior acoustic enhancement), target-type masses (63%), and masses larger than 5 cm (81.5%).

CONCLUSIONS

Posterior acoustic enhancement is present to some degree in almost half of hepatocellular carcinomas, which may relate to the tissue characteristics of the tumor or the cirrhotic liver itself. Attention to this finding, including scanning without spatial compounding, is recommended during sonographic screening for hepatocellular carcinoma in the growing population of patients with liver disease.

How long have I had my cancer, doctor? Estimating tumor age via Collins' law

To estimate the"age" of cancers at the time of diagnosis, we reviewed data on the "time to local/regional recurrence" (LRF) following initial surgical resection for three common cancers, then applied a modified version of Collins' law. We conducted a systematic review of English medical literature to identify studies reporting LRF rates, over time, following surgery alone for breast, lung, or colorectal cancer. Patients who received radiation/hormones/chemotherapy were excluded since these therapies may alter tumor growth kinetics after surgery. For each disease, data were considered in three ways: 1) absolute cumulative LRF rate over time; 2) percentage of LRFs manifest over time (to facilitate comparisons between studies with different absolute magnitudes of LRFs); and 3) weighted average of the percentage of LRFs manifest over time. For breast cancer (based on data from 3043 patients from 5 studies), we found that the median time to LRF was 2.7 years. For lung cancer (based on data from 1190 patients from 4 studies), the median time to LRF was 1.5 years. For rectal cancer (based on data from 3334 patients from 10 studies), the median time to LRF was 1.5 years. Based on Collins' law, the distribution of time to LRF suggests that the age of most of the solid tumors studied was 3 to 6 years.

Design of dynamic Hohlraum opacity samples to increase measured sample density on Z

We are attempting to measure the transmission of iron on Z at plasma temperatures and densities relevant to the solar radiation and convection zone boundary. The opacity data published by us to date has been taken at an electron density about a factor of 10 below the 9×10(22)/cm(3) electron density of this boundary. We present results of two-dimensional (2D) simulations of the heating and expansion of an opacity sample driven by the dynamic Hohlraum radiation source on Z. The aim of the simulations is to design foil samples that provide opacity data at increased density. The inputs or source terms for the simulations are spatially and temporally varying radiation temperatures with a Lambertian angular distribution. These temperature profiles were inferred on Z with on-axis time-resolved pinhole cameras, x-ray diodes, and bolometers. A typical sample is 0.3 μm of magnesium and 0.078 μm of iron sandwiched between 10 μm layers of plastic. The 2D LASNEX simulations indicate that to increase the density of the sample one should increase the thickness of the plastic backing.

Data processing of absorption spectra from photoionized plasma experiments at Z

We discuss the processing of x-ray absorption spectra from photoionized plasma experiments at Z. The data was recorded with an imaging spectrometer equipped with two elliptically bent potassium acid phthalate (KAP) crystals. Both time-integrated and time-resolved data were recorded. In both cases, the goal is to obtain the transmission spectra for quantitative analysis of plasma conditions.

Investigation of temporal changes of abuse and misuse of prescription opioids

We analyzed intentional exposures to prescription opioids (buprenorphine, fentanyl, hydrocodone, hydromorphone, morphine, methadone and Oxycodone) using the Research Abuse, Diversion and Addiction-Related Surveillance System (RADARS) Poison Center data over a 5 year period 2003-2007 to see if there were temporal trends in the abuse and misuse of prescription drugs associated with (1) weekends vs. weekdays and (2) during select holiday periods vs. non-holiday periods. Over the study period 25 of 120 holiday period days showed a decrease of at least 1 SD from the mean and 9 of 120 holiday period days showed an increase of at least 1 SD from the mean. Over the study period there were 144,653 intentional exposures. Mean percent of cases by day of week ranged from 14.03% to 14.39%, with slightly higher use on weekend days. There was no significant difference when evaluating prevalence of intentional exposures by day of week (p = 0.99). There was no significant difference when evaluating weekend versus weekday (p > 0.05). In summary, the prevalence of abuse and misuse of prescription drugs was not impacted by day of the week or difference between weekday and weekend. The impact of 8 traditional holidays appeared to be associated with a minor decrease in abuse and misuse of prescription drugs. No temporally related increase in abuse and misuse of prescription drugs was noted and conversely a trend toward decreased abuse and misuse of prescription drugs was suggested.

Mathematical modeling of a single-cell enzyme assay

A quantitative assay of beta-galactosidase activity in single cells of Saccharomyces cerevisiae has been developed using a fluorogenic substrate and flow cytometry [reported in Wittrup & Bailey, Cytometry, 9,394 (1988)]. The beta-galactosidase activity is expressed in yeast from the Escherichia coli lacZ gene under the control of the yeast GAL10 promoter, and is used as a marker for multicopy plasmid content. A nonfluorescent fluorogenic substrate is enzymatically cleaved by intracellular beta-galactosidase to form a fluorescent product. The accumulation of fluorescent product in single cells was found to depend on bulk substrate concentration and single-cell enzyme activity in a fashion that could not be described by a Michaelis-Menten kinetic rate form. It has been demonstrated that diffusion limitation rather than enzyme activity can determine the level of single-cell fluorescence under certain assay conditions, and a mathematical model has; been formulated which accounts for substrate and product diffusion. Guided by the mathematical model, the assay conditions were modified to allow measurement of single-cell enzyme activity rather than diffusion rates.

Modeling the population dynamics of baculovirus-infected insect cells: Optimizing infection strategies for enhanced recombinant protein yields

The insect cell-baculovirus model presented here is capable of simulating cell population dynamics, extracellular virion densities, and heterologous product titers in reasonable agreement with experimental data for a wide rang of multiplicities of infection (MOI) and times of infection. The model accounts for the infection of a single cell by multiple virions and the consequences on the time course of infection. The probability of infection by more than one virion was approximated using the Poisson distribution, which proved to be a refinement over second-order kinetics. The model tracks initiation and duration of important events in the progression of infected cell development (virus replication, recombinant protein synthesis, and cell lysis) for subpopulations delineated by the time and extent of their initial infection. The model suggests infection strategies, weighing the importance of MOI and infection time. Maximum product titers result from infection in the early exponential growth phase with low MOI.

Effect of alteration of the acetic acid synthesis pathway on the fermentation pattern of escherichia coli

The glucose metabolism of an Escherichia coli strain bearing mutations abolishing both acetyl phosphotransferase (PTA) and acetate kinase (ACK) activities was studied under aerobic and anaerobic conditions. These studies were conducted in a complex medium with the mutant carrying no plasmid, the mutant carrying the common cloning vector pUC19, and the mutant carrying a plasmid bearing the "pet" operon that encodes Zymomonas mobilis pyruvate decarboxylase and alcohol dehydrogenase activities. The mutant carrying no plasmid showed lower specific growth and glucose uptake rates relative to the parent wild-type strain (K-12), Lactic acid was produced at higher levels than the wild type, and considerable amounts of pyruvic acid were secreted as an unusual byproduct. Analysis of other fermentation products showed low but significant amounts of acetic acid, no accumulation of formic acid, and lower secretion of succinate and ethanol. The maintenance of the plasmid pUC19 in the mutant negatively affected metabolism. Expression of the pet operon overcame the metabolic stress caused by the plasmid, enhancing growth and glucose uptake rates to the values observed in the plasmidfree mutant. Also, expression of the pet operon allowed consumption of pyruvate accumulated during the first hours of fermentation.