Integration of enzyme activities into metabolic flux distributions by elementary mode analysis

<p>Abstract</p> <p>Background</p> <p>In systems biology, network-based pathway analysis facilitates understanding or designing metabolic systems and enables prediction of metabolic flux distributions. Network-based flux analysis requires considering not only pathway architectures but also the proteome or transcriptome to predict flux distributions, because recombinant microbes significantly change the distribution of gene expressions. The current problem is how to integrate such heterogeneous data to build a network-based model.</p> <p>Results</p> <p>To link enzyme activity data to flux distributions of metabolic networks, we have proposed Enzyme Control Flux (ECF), a novel model that integrates enzyme activity into elementary mode analysis (EMA). ECF presents the power-law formula describing how changes in enzyme activities between wild-type and a mutant are related to changes in the elementary mode coefficients (EMCs). To validate the feasibility of ECF, we integrated enzyme activity data into the EMCs of <it>Escherichia coli </it>and <it>Bacillus subtilis </it>wild-type. The ECF model effectively uses an enzyme activity profile to estimate the flux distribution of the mutants and the increase in the number of incorporated enzyme activities decreases the model error of ECF.</p> <p>Conclusion</p> <p>The ECF model is a non-mechanistic and static model to link an enzyme activity profile to a metabolic flux distribution by introducing the power-law formula into EMA, suggesting that the change in an enzyme profile rather reflects the change in the flux distribution. The ECF model is highly applicable to the central metabolism in knockout mutants of <it>E. coli </it>and <it>B. subtilis</it>.</p

A suitable stereoisomer of vibrioferrin probes for iron uptake of Vibrio parahaemolyticus

Suitable Stereostructures of vibrioferrin probes for iron uptake of Vibrio parahaemolyticus was revealed. Stereoisomers of dansyl labeled vibrioferrin at the 2′′-position were synthesized and their uptake activities were evaluated. Vibrio parahaemolyticus take in both isomers at the 2′′-position. In addition to Vibrio parahaemolyticus, several bacteria have also taken up the (R)-isomer

Diagnostic value of texture analysis of apparent diffusion coefficient maps for differentiating fat-poor angiomyolipoma from non-clear-cell renal cell carcinoma

Purpose: To investigate the feasibility of texture analysis of apparent diffusion coefficient (ADC) maps for differentiating fat-poor angiomyolipomas (fpAMLs) from non-clear-cell renal cell carcinomas (non-ccRCCs). Methods: In this bi-institutional study, we included two consecutive cohorts from different institutions with pathologically confirmed solid renal masses: 67 patients (fpAML = 46; non-ccRCC = 21) for model development and 39 (fpAML = 24; non-ccRCC = 15) for validation. Patients underwent preoperative magnetic resonance imaging (MRI), including diffusion-weighted imaging. We extracted 45 texture features using a software with volumes of interest on ADC maps. Receiver operating characteristic curve analysis was performed to compare the diagnostic performance between the random forest (RF) model (derived from extracted texture features) and conventional subjective evaluation using computed tomography and MRI by radiologists. Results: RF analysis revealed that grey-level zone length matrix long-zone high grey-level emphasis was the dominant texture feature for diagnosing fpAML. The area under the curve (AUC) of the RF model to distinguish fpAMLs from non-ccRCCs was not significantly different between the validation and development cohorts (p = .19). In the validation cohort, the AUC of the RF model was similar to that of board-certified radiologists (p = .46) and significantly higher than that of radiology residents (p = .03). Conclusions: Texture analysis of ADC maps demonstrated similar diagnostic performance to that of board-certified radiologists for discriminating between fpAMLs and non-ccRCCs. Diagnostic performances in the development and validation cohorts were comparable despite using data from different imaging device manufacturers and institutions

In Vivo Function and Evolution of the Eutherian-Specific Pluripotency Marker UTF1

Embryogenesis in placental mammals is sustained by exquisite interplay between the embryo proper and placenta. UTF1 is a developmentally regulated gene expressed in both cell lineages. Here, we analyzed the consequence of loss of the UTF1 gene during mouse development. We found that homozygous UTF1 mutant newborn mice were significantly smaller than wild-type or heterozygous mutant mice, suggesting that placental insufficiency caused by the loss of UTF1 expression in extra-embryonic ectodermal cells at least in part contributed to this phenotype. We also found that the effects of loss of UTF1 expression in embryonic stem cells on their pluripotency were very subtle. Genome structure and sequence comparisons revealed that the UTF1 gene exists only in placental mammals. Our analyses of a family of genes with homology to UTF1 revealed a possible mechanism by which placental mammals have evolved the UTF1 genes.This study was supported in part by the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT), and mostly by the Support Program for the Strategic Research Foundation at Private Universities, 2008–2012. This study was performed as a part of the Core Research for Evolutional Science and Technology (CREST) Agency. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Ratiometric fluorescence imaging of cell surface pH by poly(ethylene glycol)-phospholipid conjugated with fluorescein isothiocyanate

Various physiological and pathological processes are accompanied with the alteration of pH at extracellular juxtamembrane region. Accordingly, the methods to analyze the cell surface pH have been demanded in biological and medical sciences. In this study, we have established a novel methodology for cell surface pH imaging using poly(ethylene glycol)-phospholipid (PEG-lipid) as a core structure of ratiometric fluorescent probes. PEG-lipid is a synthetic amphiphilic polymer originally developed for the cell surface modification in transplantation therapy. Via its hydrophobic alkyl chains of the phospholipid moiety, PEG-lipid is, when applied extracellularly, spontaneously inserted into the plasma membrane and retained at the surface of the cells. We have demonstrated that the PEG-lipid conjugated with fluorescein isothiocyanate (FITC-PEG-lipid) can be used as a sensitive and reversible cell-surfacea-nchored pH probe between weakly alkaline and acidic pH with an excellent spatiotemporal resolution. The remarkably simple procedure for cell-surface labeling with FITC-PEG-lipid would also be advantageous when considering its application to high-throughput in vitro assay. This study further indicates that various probes useful for the investigation of juxtamembrane environments could also be developed by using PEG-lipid as the core structure for bio-membrane anchoring

The Composition and Structure of Biofilms Developed by Propionibacterium acnes Isolated from Cardiac Pacemaker Devices

The present study aimed to understand the biofilm formation mechanism of Propionibacterium acnes by analyzing the components and structure of the biofilms. P. acnes strains were isolated from the surface of explanted cardiac pacemaker devices that exhibited no clinical signs of infection. Culture tests using a simple stamp culture method (pressing pacemakers against the surface of agar plates) revealed frequent P. acnes colonization on the surface of cardiac pacemaker devices. P. acnes was isolated from 7/31 devices, and the isolates were categorized by multilocus sequence typing into five different sequence types (STs): ST4 (JK18.2), ST53 (JK17.1), ST69 (JK12.2 and JK13.1), ST124 (JK5.3), ST125 (JK6.2), and unknown ST (JK19.3). An in vitro biofilm formation assay using microtiter plates demonstrated that 5/7 isolates formed biofilms. Inhibitory effects of DNase I and proteinase K on biofilm formation varied among isolates. In contrast, dispersin B showed no inhibitory activity against all isolates. Three-dimensional live/dead imaging of P. acnes biofilms with different biochemical properties using confocal laser microscopy demonstrated different distributions and proportions of living and dead cells. Additionally, it was suggested that extracellular DNA (eDNA) plays a role in the formation of biofilms containing living cells. Ultrastructural analysis of P. acnes biofilms using a transmission electron microscope and atmospheric scanning electron microscope revealed leakage of cytoplasmic components along with cell lysis and fibrous structures of eDNA connecting cells. In conclusion, the biochemical properties and structures of the biofilms differed among P. acnes isolates. These findings may provide clues for establishing countermeasures against biofilm-associated infection by P. acnes

Atherosclerosis of the right posterior hepatic artery in a patient with hilar cholangiocarcinoma undergoing left trisectionectomy: a case report of a therapeutic pitfall

Abstract Background We experienced a rare case of benign arterial stricture of the right posterior hepatic artery (RPHA) caused by atherosclerosis in a patient with hilar cholangiocarcinoma. Case presentation A 75-year-old man was referred to our hospital for the detailed investigation of serum hepatobiliary enzyme elevation. The patient had a history of hypertension, type 2 diabetes mellitus, and an operative history of coronary artery bypass grafting 10 years before. Endoscopic retrograde cholangiography found strictures of the right and left hepatic ducts with involvement of right anterior and posterior bile ducts. Adenocarcinoma was evident by brush cytology. We diagnosed these findings as hilar cholangiocarcinoma and planned left trisectionectomy including bile duct reconstruction. Although the tumor and RPHA were not adjacent, preoperative multidetector computed tomography revealed a stricture of the RPHA that was 5.6 mm in length. We suspected that atherosclerosis caused the stricture, and we performed digital subtraction angiography and intravascular ultrasonography that showed stricture of the RPHA accompanied by thick plaques in the arterial wall. We placed a bare-metal stent in the RPHA and then performed left trisectionectomy. Since this patient developed bile leakage postoperatively, percutaneous drainage was performed. The bile leakage was successfully controlled, and the patient was discharged 3 months after surgery. Unfortunately, 4 months after hepatectomy, he was re-hospitalized with multiple pyogenic liver abscesses. We performed intensive multimodal treatment for the liver abscesses and stabilized the disease; however, we eventually lost this patient due to liver failure 14 months after surgery. Conclusion To the best of our knowledge, there is no previous literature on atherosclerosis of the RPHA, which was evident preoperatively in our case. Because arterial complications may lead to critical biliary complications in patients who undergo left trisectionectomy, we first performed prophylactic arterial stent placement. We speculate that existing chronic microscopic injury of the peribiliary plexus might have caused the liver abscesses. We successfully diagnosed atherosclerosis of the RPHA preoperatively. However, further investigation of patients is warranted to determine if left trisectionectomy is contraindicated in these patients

18F-Labeled Pyrido[3,4-d]pyrimidine as an Effective Probe for Imaging of L858R Mutant Epidermal Growth Factor Receptor.

In nonsmall-cell lung carcinoma patients, L858R mutation of epidermal growth factor receptor (EGFR) is often found, and molecular target therapy using EGFR tyrosine kinase inhibitors is effective for the patients. However, the treatment frequently develops drug resistance by secondary mutation, of which approximately 50% is T790M mutation. Therefore, the ability to predict whether EGFR will undergo secondary mutation is extremely important. We synthesized a novel radiofluorinated 4-(anilino)pyrido[3,4-d]pyrimidine derivative ([18F]APP-1) and evaluated its potential as a positron emission tomography (PET) imaging probe to discriminate the difference in mutations of tumors. EGFR inhibition assay, cell uptake, and biodistribution study showed that [18F]APP-1 binds specifically to the L858R mutant EGFR but not to the L858R/T790M mutant. Finally, on PET imaging study using [18F]APP-1 with tumor-bearing mice, the H3255 tumor (L858R mutant) was more clearly visualized than the H1975 tumor (L858R/T790M mutant)