Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism.

BACKGROUND AND OBJECTIVES: Metabolomics studies have revealed transition points in metabolic signatures of red cells during storage in SAGM, whose clinical significance is unclear. We set out to investigate whether these transition points occur independent of storage media and define differences in the metabolism of red cells in additive solutions. MATERIALS AND METHODS: Red cell concentrates were stored in SAGM, AS-1, AS-3 or PAGGSM, and sampled fourteen times spanning Day 1-46. Following quality control, the samples were split into extracellular and intracellular aliquots. These were analysed with ultra-high-performance liquid chromatography coupled to mass spectrometry analysis affording quantitative metabolic profiles of both intra- and extracellular red cell metabolites. RESULTS: Differences were observed in glycolysis, purine salvage, glutathione synthesis and citrate metabolism on account of the storage solutions. Donor variability however hindered the accurate characterization of metabolic transition time-points. Intracellular citrate concentrations were increased in red cells stored in AS-3 and PAGGSM media. The metabolism of citrate in red cells in SAGM was subsequently confirmed using 13 C citrate isotope labelling and shown to originate from citrate anticoagulant. CONCLUSION: Metabolic signatures that discriminate between 'fresh' and 'old' stored red cells are dependent upon additive solutions. Specifically, the incorporation and metabolism of citrate in additive solutions with lower chloride ion concentration is altered and impacts glycolysis.

Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits.

Strains across the Lactobacillaceae family form the basis for a trillion-dollar industry. Our understanding of the genomic basis for their key traits is fragmented, however, including the metabolism that is foundational to their industrial uses. Pangenome analysis of publicly available Lactobacillaceae genomes allowed us to generate genome-scale metabolic network reconstructions for 26 species of industrial importance. Their manual curation led to more than 75,000 gene-protein-reaction associations that were deployed to generate 2,446 genome-scale metabolic models. Cross-referencing genomes and known metabolic traits allowed for manual metabolic network curation and validation of the metabolic models. As a result, we provide the first pangenomic basis for metabolism in the Lactobacillaceae family and a collection of predictive computational metabolic models that enable a variety of practical uses.IMPORTANCELactobacillaceae, a bacterial family foundational to a trillion-dollar industry, is increasingly relevant to biosustainability initiatives. Our study, leveraging approximately 2,400 genome sequences, provides a pangenomic analysis of Lactobacillaceae metabolism, creating over 2,400 curated and validated genome-scale models (GEMs). These GEMs successfully predict (i) unique, species-specific metabolic reactions; (ii) niche-enriched reactions that increase organism fitness; (iii) essential media components, offering insights into the global amino acid essentiality of Lactobacillaceae; and (iv) fermentation capabilities across the family, shedding light on the metabolic basis of Lactobacillaceae-based commercial products. This quantitative understanding of Lactobacillaceae metabolic properties and their genomic basis will have profound implications for the food industry and biosustainability, offering new insights and tools for strain selection and manipulation.

Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing.

As the availability of data sets increases, meta-analysis leveraging aggregated and interoperable data types is proving valuable. This study leveraged a meta-analysis workflow to identify mutations that could improve robustness to reactive oxygen species (ROS) stresses using an industrially important melatonin production strain as an example. ROS stresses often occur during cultivation and negatively affect strain performance. Cellular response to ROS is also linked to the SOS response and resistance to pH fluctuations, which is important to strain robustness in large-scale biomanufacturing. This work integrated more than 7000 E. coli adaptive laboratory evolution (ALE) mutations across 59 experiments to statistically associate mutated genes to 2 ROS tolerance ALE conditions from 72 unique conditions. Mutant oxyR, fur, iscR, and ygfZ were significantly associated and hypothesized to contribute fitness in ROS stress. Across these genes, 259 total mutations were inspected in conjunction with transcriptomics from 46 iModulon experiments. Ten mutations were chosen for reintroduction based on mutation clustering and coinciding transcriptional changes as evidence of fitness impact. Strains with mutations reintroduced into oxyR, fur, iscR, and ygfZ exhibited increased tolerance to H2O2 and acid stress and reduced SOS response, all of which are related to ROS. Additionally, new evidence was generated toward understanding the function of ygfZ, an uncharacterized gene. This meta-analysis approach utilized aggregated and interoperable multiomics data sets to identify mutations conferring industrially relevant phenotypes with the least drawbacks, describing an approach for data-driven strain engineering to optimize microbial cell factories.

Using the reconstructed genome-scale human metabolic network to study physiology and pathology.

Metabolism plays a key role in many major human diseases. Generation of high-throughput omics data has ushered in a new era of systems biology. Genome-scale metabolic network reconstructions provide a platform to interpret omics data in a biochemically meaningful manner. The release of the global human metabolic network, Recon 1, in 2007 has enabled new systems biology approaches to study human physiology, pathology and pharmacology. There are currently more than 20 publications that utilize Recon 1, including studies of cancer, diabetes, host-pathogen interactions, heritable metabolic disorders and off-target drug binding effects. In this mini-review, we focus on the reconstruction of the global human metabolic network and four classes of its application. We show that computational simulations for numerous pathologies have yielded clinically relevant results, many corroborated by existing or newly generated experimental data.

A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.

We derive a convex optimization problem on a steady-state nonequilibrium network of biochemical reactions, with the property that energy conservation and the second law of thermodynamics both hold at the problem solution. This suggests a new variational principle for biochemical networks that can be implemented in a computationally tractable manner. We derive the Lagrange dual of the optimization problem and use strong duality to demonstrate that a biochemical analogue of Tellegen's theorem holds at optimality. Each optimal flux is dependent on a free parameter that we relate to an elementary kinetic parameter when mass action kinetics is assumed.

Multicentre prospective study of fascial closure rate after open abdomen with vacuum and mesh-mediated fascial traction.

BACKGROUND: Damage control surgery and temporary open abdomen (OA) have been adopted widely, in both trauma and non-trauma situations. Several techniques for temporary abdominal closure have been developed. The main objective of this study was to evaluate the fascial closure rate in patients after vacuum-assisted wound closure and mesh-mediated fascial traction (VAWCM) for long-term OA treatment, and to describe complications. METHODS: This prospective study included all patients who received VAWCM treatment between 2006 and 2009 at four hospitals. Patients with anticipated OA treatment for fewer than 5 days and those with non-midline incisions were excluded. RESULTS: Among 151 patients treated with an OA, 111 received VAWCM treatment. Median age was 68 years. Median OA treatment time was 14 days. Main disease aetiologies were vascular (45 patients), visceral surgical disease (57) and trauma (9). The fascial closure rate was 76·6 per cent in intention-to-treat analysis and 89 per cent in per-protocol analysis. Eight patients developed an intestinal fistula, of whom seven had intestinal ischaemia. Intestinal fistula was an independent factor associated with failure of fascial closure (odds ratio (OR) 8·55, 95 per cent confidence interval 1·47 to 49·72; P = 0·017). The in-hospital mortality rate was 29·7 per cent. Age (OR 1·21, 1·02 to 1·43; P = 0·027) and failure of fascial closure (OR 44·50, 1·13 to 1748·52; P = 0·043) were independently associated with in-hospital mortality. CONCLUSION: The VAWCM method provided a high fascial closure rate after long-term treatment of OA. Technique-related complications were few. No patient was left with a large planned ventral hernia.

Biomass as a source of chemical feedstocks: an economic evaluation.

It is suggested that the raw materials and technology exist for basing a major fraction of the U.S. chemical industry on four fermentation products, used in the proper portions: ethanol, isopropanol, n-butanol, and 2,3-butanediol. The primary route for introduction of these materials is dehydration of the alcohols and diols to olefins, which would cause little disruption of the existing industry downstream from the olefins. The proposed substitution has the advantages that it would provide a smooth transition toward renewable feedstocks, while decreasing dependence on fossil sources of organic material and use of toxic materials. However, to make these materials attractive as feedstocks or intermediates in chemical production, their current prices must be substantially reduced. Even with the optimum mix, their largeseale utilization will only occur at about 20 to 40 percent of their estimated chemical prices.

Metabolic modeling of microbial strains in silico.

The large volume of genome-scale data that is being produced and made available in databases on the World Wide Web is demanding the development of integrated mathematical models of cellular processes. The analysis of reconstructed metabolic networks as systems leads to the development of an in silico or computer representation of collections of cellular metabolic constituents, their interactions and their integrated function as a whole. The use of quantitative analysis methods to generate testable hypotheses and drive experimentation at a whole-genome level signals the advent of a systemic modeling approach to cellular and molecular biology.

In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

A significant goal in the post-genome era is to relate the annotated genome sequence to the physiological functions of a cell. Working from the annotated genome sequence, as well as biochemical and physiological information, it is possible to reconstruct complete metabolic networks. Furthermore, computational methods have been developed to interpret and predict the optimal performance of a metabolic network under a range of growth conditions. We have tested the hypothesis that Escherichia coli uses its metabolism to grow at a maximal rate using the E. coli MG1655 metabolic reconstruction. Based on this hypothesis, we formulated experiments that describe the quantitative relationship between a primary carbon source (acetate or succinate) uptake rate, oxygen uptake rate, and maximal cellular growth rate. We found that the experimental data were consistent with the stated hypothesis, namely that the E. coli metabolic network is optimized to maximize growth under the experimental conditions considered. This study thus demonstrates how the combination of in silico and experimental biology can be used to obtain a quantitative genotype-phenotype relationship for metabolism in bacterial cells.

The physico-chemical factors that govern retrovirus-mediated gene transfer.

The most commonly used vehicle for gene transfer into human target cells is a replication incompetent retroviral vector. The efficiency of gene transfer with this type of vector has proven to be too low to implement effective gene therapy. To date much effort has gone into engineering the genetic and biochemical functionalities of retroviral vectors. Although progress has been achieved, high-efficiency reproducible gene transfer into human cells remains elusive. There are many important physico-chemical and systemic kinetic factors that govern the process of retrovirus-mediated gene transfer. These factors have gone mostly unrecognized to date. The former include the nature of the random Brownian motion of the retrovirus and the physico-chemical forces that determine the binding of the retroviral vector to the target cell. The latter arise from the kinetics of virus binding and entry into the target cell, as well as the kinetic interplay between cell-cycle and retroviral life-cycle events that determine the intracellular fate of the virus. This review describes these processes and how they constrain the efficiency of the gene transfer process.

Growth factor consumption and production in perfusion cultures of human bone marrow correlate with specific cell production.

Perfusion cultures of human bone marrow mononuclear cells (BMMNC) provide a unique in vitro model of hematopoiesis, supporting growth of both accessory and hematopoietic elements. In this study, bioreactors were used to analyze the consumption and production of growth factors (GFs) in relation to each other and to the cells produced. The exogenously added GFs interleukin-3 (IL-3), granulocyte-macrophage colony-stimulating factor (GM-CSF), stem cell factor (SCF), and erythropoietin (Epo) each exhibited different, but reproducible, consumption kinetics. Epo and IL-3 were consumed slowly for the first 5-7 days, and then the consumption rate of both increased. Epo consumption reached a plateau by day 10, whereas IL-3 consumption continued to increase. Consumption of SCF was similar to that of Epo, but began 2-3 days earlier. GM-CSF was consumed throughout the culture period in an accelerating manner. Consumption of SCF and Epo were related, because omission of Epo from the growth medium reduced SCF consumption by 53% and omission of SCF reduced Epo consumption by 82%. A reproducible relationship between cumulative GF consumption and total cell production was observed. Epo was most potent, with 5900 molecules consumed per cell produced, whereas 69,400 molecules of SCF were consumed per cell generated. More specifically, Epo consumption was correlated (r = 0.92 and 0.96) with the number of glycophorin A-positive (glyA+) cells produced, and the rate of Epo consumption varied with the progression of cells through the erythroid lineage. Consequently, measurement of GF consumption rates may be useful for quantifying the types of cells present in a culture. Endogenous GF production was also examined. G-CSF and MIP-1 alpha were present at high levels during the first 4 days but then declined rapidly. LIF first appeared in the second week and steadily increased thereafter. Omission of SCF from the medium allowed the detection of endogenous SCF production, and the kinetics was similar to that of LIF. IL-6 production was biphasic, with a peak and decline in week 1 and an increase during week 2. TGF-beta was below the level of detection in these cultures. The results suggest that perfusion supports accessory and hematopoietic elements which interact and therefore represent a partially functional tissue ex vivo. This system provides a useful model for studying relationships within GF networks and for elucidating the conditions that result in primitive cell expansion ex vivo.

Can Dexter cultures support stem cell proliferation?

The in vitro culture of mouse bone marrow (Dexter cultures) has allowed a detailed analysis of the biology of murine hematopoiesis. However, attempts to develop stable long-term human bone marrow cultures have been unsuccessful. Available culture systems all have finite and relatively short lifetimes. The reasons for the limited longevity are unknown. Utilizing computer-assisted integration techniques, we have theoretically simulated culture cell production kinetics to help identify factors that may be responsible for culture decay, as well as to suggest possible means of improving culture longevity. The simulation demonstrates that removal of stem cells is a possible mechanism leading to culture decline. Under the standard bone marrow culture conditions, even with a high stem cell renewal rate, the cultures appear to be destined to fail. Thus, the development of proper sampling techniques or improved stem cell retention may be critical to obtain successful long-term cultures.

Flow cytometric analysis of human bone marrow perfusion cultures: erythroid development and relationship with burst-forming units-erythroid.

Flow cytometry has been used in recent years to study antigenic and physical changes accompanying hematopoietic cell differentiation. Such studies have provided the basis for rapid and objective assays that are potential alternatives to the colony assays currently in widespread use. In this report, erythropoiesis was examined in growth factor-supplemented perfused cultures of bone marrow mononuclear cells (BMMNC) using flow cytometric analysis of the transferrin receptor (CD71), glycophorin antigen expression occurred with time, Initially, fewer than 10% of the cells were (CD71++, but by day 8, 19-34% of the cells were CD71++gly A-. This was followed by the appearance of gly A on 10-60% of the CD71++ cells. After day 10, CD71 expression on many gly A+ cells decreased so that a population of CD71-gly A+ cells (11-54 accumulated by day 14. Each phenotype was sorted for morphologic identification and colony assay analysis. CD71++gly A- cells were 85% blasts, one-half of which were erythroblasts, and were significantly enriched for burst-forming units-erythroid (BFU-E). The time-varying number of CD71++gly A- cells in these cultures was found to correlate with the number of BF.78-0.97). Three-color analysis was next used to examine CD33 expression on BFU-E, and in fresh BM, most were found to be CD33-. During culture, however, the number of BFU-E recovered from CD33+ populations first increased and then decreased. Therefore, CD33 was not particularly useful for identifying BFU-E. In contrast, CFU-GM were mostly found to be in the CD71+CD33+ population throughout the culture period. When erythropoietin (Epo) was not added to these cultures, the percentage of gly A+ cells was reduced from 33 to 3.3%. Further, the omission of Epo caused an 80% decrease in the number of BFU-E and a corresponding 94% decrease in the number of CD71++gly A- cells, thereby maintaining the relationship between CD71++gly A- cells and BFU-E. Therefore, flow cytometric analysis was found to be useful in assessing erythroid development, and this approach may be used to develop flow cytometric assays for other populations of interest in hematopoietic cell cultures.

Consistent and high rates of gene transfer can be obtained using flow-through transduction over a wide range of retroviral titers.

Flow-through transduction methods have been developed to overcome physical limitations imposed by Brownian motion on retroviral delivery. This method uses net fluid flow of retroviral supernatants through a porous membrane on which the target cells are placed. It is shown that in comparison to static transduction methods, flow-through transductions have the following advantages: (i) flow-through transductions lead to transduction rates that exceed those obtained by static transduction; (ii) flow-through transductions lead to high transduction rates even at low viral concentrations, eliminating many of the concerns associated with the production of high-titer virus supernatants; (iii) flow-through transductions are insensitive to viral titers, eliminating the need to produce consistently retroviral supernatants at given virus concentrations; (iv) flow-through transductions can be carried out without the use of polycations, such as polybrene; and (v) the volume of viral supernatants needed for gene transfer can be sharply reduced. Taken together, these advantages of flow-through transductions are likely to lead to their widespread use for gene transfer work, both in research and clinical settings.

Coupled effects of polybrene and calf serum on the efficiency of retroviral transduction and the stability of retroviral vectors.

The relative concentrations of Polybrene (PB) and calf serum (CS) in retroviral supernatant have considerable effects on the efficiency of retrovirus-mediated gene transfer and the stability of retroviral vectors. The effect of PB on the efficiency of transduction of Moloney murine leukemia virus (MMuLV)-derived vectors is strongly dependent on CS. At a fixed CS concentration, the efficiency of transduction shows a maximum as a function of PB concentration. Increasing the CS concentration shifted this maximum to higher PB concentrations, but the value of the maximum remained the same. Therefore, there were optimal combinations of PB and CS concentrations that maximized the efficiency of gene transfer: 4.4, 8.8, 13.2, and 22 micrograms/ml of PB for 1%, 2.5%, 5%, and 10% (vol/vol) CS, respectively. Moreover, the presence of PB affected significantly the kinetics of retroviral decay. The loss of retroviral activity did not follow simple exponential decay in the absence of PB during the decay period of the viral supernatant. The dynamics of viral inactivation showed an initial phase during which the transduction efficiency remained constant followed by exponential decay. However, in the presence of high PB concentrations (13.2 micrograms/ml) during the decay period of retroviral vectors, the initial delay was lost and the decay was exponential right from the outset. The present results suggest that in addition to virus-cell interactions that occur on the target cell surface, other physico-chemical processes may occur in solution that have profound effect on retroviral activity and therefore they are of particular importance for gene therapy.

Retroviral infection is limited by Brownian motion.

Replication-defective retroviruses are frequently used as gene carriers for gene transfer into target cells. Here we show that the short half-lives of retroviruses limit the distance that they can effectively travel in solution by Brownian motion, and thus the possibility of successful gene transfer. This physiochemical limitation can be overcome, and effective contact between the retroviral gene carrier and the target cell can be obtained, by using net convective flow of retrovirus-containing medium through a layer of target cells. Using model cell lines (NIH-3T3 and CV-1), it was shown that gene transfer rates can be increased by more than an order of magnitude using the same concentration infection medium. High transduction rates could be obtained even in the absence of polycations, such as Polybrene, which heretofore have been required to achieve reasonable transduction rates. This development may play an important role in realizing human gene therapy.

Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.

BACKGROUND: Genome sequencing and bioinformatics are producing detailed lists of the molecular components contained in many prokaryotic organisms. From this 'parts catalogue' of a microbial cell, in silico representations of integrated metabolic functions can be constructed and analyzed using flux balance analysis (FBA). FBA is particularly well-suited to study metabolic networks based on genomic, biochemical, and strain specific information. RESULTS: Herein, we have utilized FBA to interpret and analyze the metabolic capabilities of Escherichia coli. We have computationally mapped the metabolic capabilities of E. coli using FBA and examined the optimal utilization of the E. coli metabolic pathways as a function of environmental variables. We have used an in silico analysis to identify seven gene products of central metabolism (glycolysis, pentose phosphate pathway, TCA cycle, electron transport system) essential for aerobic growth of E. coli on glucose minimal media, and 15 gene products essential for anaerobic growth on glucose minimal media. The in silico tpi-, zwf, and pta- mutant strains were examined in more detail by mapping the capabilities of these in silico isogenic strains. CONCLUSIONS: We found that computational models of E. coli metabolism based on physicochemical constraints can be used to interpret mutant behavior. These in silica results lead to a further understanding of the complex genotype-phenotype relation.

A genome-wide scan for preeclampsia in the Netherlands.

Preeclampsia, hallmarked by de novo hypertension and proteinuria in pregnancy, has a familial tendency. Recently, a large Icelandic genome-wide scan provided evidence for a maternal susceptibility locus for preeclampsia on chromosome 2p13 which was confirmed by a genome scan from Australia and New Zealand (NZ). The current study reports on a genome-wide scan of Dutch affected sib-pair families. In total 67 Dutch affected sib-pair families, comprising at least two siblings with proteinuric preeclampsia, eclampsia or HELLP-syndrome, were typed for 293 polymorphic markers throughout the genome and linkage analysis was performed. The highest allele sharing lod score of 1.99 was seen on chromosome 12q at 109.5 cM. Two peaks overlapped in the same regions between the Dutch and Icelandic genome-wide scan at chromosome 3p and chromosome 15q. No overlap was seen on 2p. Re-analysis in 38 families without HELLP-syndrome (preeclampsia families) and 34 families with at least one sibling with HELLP syndrome (HELLP families), revealed two peaks with suggestive evidence for linkage in the non-HELLP families on chromosome 10q (lod score 2.38, D10S1432, 93.9 cM) and 22q (lod score 2.41, D22S685, 32.4 cM). The peak on 12q appeared to be associated with HELLP syndrome; it increased to a lod score of 2.1 in the HELLP families and almost disappeared in the preeclampsia families. A nominal peak on chromosome 11 in the preeclampsia families showed overlap with the second highest peak in the Australian/NZ study. Results from our Dutch genome-wide scan indicate that HELLP syndrome might have a different genetic background than preeclampsia.

Plasma concentrations of CA-50 in relation to tumour burden in exocrine pancreatic cancer.

The tumour-associated antigen CA-50 was analysed in plasma from 90 patients with cytologically verified exocrine carcinoma of the pancreas, and related to the size of the primary carcinoma, the largest metastasis of the liver and the degree of tumour-transformed liver parenchyme at 143 examinations. The median concentration of CA-50 in the patients with metastases of the liver was significantly higher than in the group lacking metastases. Spearman rank correlation test at three different levels of CA-50 (all values, exceeding 100 U/ml and exceeding 200 U/ml), showed a correlation between CA-50 and diameter of the primary pancreatic carcinoma in patients with liver metastases, but not in the group lacking liver metastases. No correlations were seen between CA-50 levels and size of liver metastasis or degree of tumour-transformed liver parenchyme. Hence, high plasma concentrations of CA-50 in patients with diagnosed or suspected exocrine pancreatic carcinoma could strongly indicate metastatic processes.

Replication of mini-F plasmids during the bacterial division cycle.

The cell-cycle replication patterns of two mini-F plasmids have been examined using the membrane-elution technique (to produce cells labelled at different times during the division cycle) and scintillation counting (for quantitative analysis of radioactivity incorporated into plasmid DNA). The mini-F plasmid pML31, which contains the oriV and oriS origins of replication, replicates in a cell-cycle-specific manner with a pattern and cell-cycle timing similar to the parental F plasmid. The mini-F plasmid pMF21, deleted for the region containing the oriV origin of replication, replicates more randomly throughout the division cycle. These results suggest that the oriV origin of replication may be related to cell-cycle-specific replication of the F plasmid.