The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a complex response to changes in nitrogen supply

The extent to which individual plants utilise nitrate and ammonium, the two principal nitrogen sources in the rhizosphere, is variable and many species require a balance between the two forms for optimal growth. The effects of nitrate and ammonium on gene expression, enzyme activity and metabolite composition have been documented extensively with the aim of understanding the way in which plant cells respond to the different forms of nitrogen, but ultimately the impact of these changes on the organisation and operation of the central metabolic network can only be addressed by analysing the fluxes supported by the network. Accordingly steady‐state metabolic flux analysis was used to define the metabolic phenotype of a heterotrophic Arabidopsis thaliana cell culture grown in Murashige and Skoog and ammonium‐free media, treatments that influenced growth and biomass composition. Fluxes through the central metabolic network were deduced from the redistribution of label into metabolic intermediates and end products observed when cells were labelled with [1‐¹³C]‐, [2‐¹³C]‐ or [¹³C₆]glucose, in tandem with ¹⁴C‐measurements of the net accumulation of biomass. Analysis of the flux maps showed that: (i) flux through the oxidative pentose phosphate pathway varied independently of the reductant demand for biosynthesis, (ii) non‐plastidic processes made a significant and variable contribution to the provision of reducing power for the plastid, and (iii) the inclusion of ammonium in the growth medium increased cell maintenance costs, in agreement with the futile cycling model of ammonium toxicity. These conclusions highlight the complexity of the metabolic response to a change in nitrogen nutrition.     

Mutation at the folate receptor 4 locus modulates gene expression profiles in the mouse uterus in response to periconceptional folate supplementation

Periconceptional supplementation of folic acid to the diet of women is considered a great success for a public health intervention. Higher folate status, either by supplementation, or via the mandatory fortification of grain products in the United States, has led to significant reduction in the incidence of neural tube defects. Besides birth defects, folate deficiency has been linked to a variety of morbidities, most notably to increased risk for cancer. However, recent evidence suggests that excess folate may be detrimental — for birth defect incidence or in the progression of cancer. How folate mediates beneficial or detrimental effects is not well understood. It is also unknown what molecular responses are elicited in women taking folate supplements, and thus experience a bolus of folate on top of the status achieved by fortification. To characterize the response to a periconceptional regimen of supplementation with folinic acid, we performed gene expression profiling experiments on uterus tissue of pregnant mice with either wildtype alleles or targeted disruption at the folate receptor 4 locus. We observed that, depending on the genetic background, folinic acid supplementation affects expression of genes that contribute to lipid metabolism, protein synthesis, mitochondrial function, cell cycle, and cell activation. The extent of the response is strongly modulated by the genetic background. Finally, we provide evidence that folinic acid supplementation in the mutant paradigm affects histone methylation status, a potential mechanism of gene regulation in this model.     

Mineral‐hosted biofilm communities in the continental deep subsurface,Deep Mine Microbial Observatory,SD, USA

Deep subsurface biofilms are estimated to host the majority of prokaryotic life on Earth, yet fundamental aspects of their ecology remain unknown. An inherent difficulty in studying subsurface biofilms is that of sample acquisition. While samples from marine and terrestrial deep subsurface fluids have revealed abundant and diverse microbial life, limited work has described the corresponding biofilms on rock fracture and pore space surfaces. The recently established Deep Mine Microbial Observatory (DeMMO) is a long‐term monitoring network at which we can explore the ecological role of biofilms in fluid‐filled fractures to depths of 1.5 km. We carried out in situ cultivation experiments with single minerals representative of DeMMO host rock to explore the ecological drivers of biodiversity and biomass in biofilm communities in the continental subsurface. Coupling cell densities to thermodynamic models of putative metabolic reactions with minerals suggests a metabolic relationship between biofilms and the minerals they colonize. Our findings indicate that minerals can significantly enhance biofilm cell densities and promote selective colonization by taxa putatively capable of extracellular electron transfer. In turn, minerals can drive significant differences in biodiversity between fluid and biofilm communities. Given our findings at DeMMO, we suggest that host rock mineralogy is an important ecological driver in deep continental biospheres.     

Strategies for investigating the plant metabolic network with steady-state metabolic flux analysis: lessons from an Arabidopsis cell culture and other systems

Steady-state (13)C metabolic flux analysis (MFA) is currently the experimental method of choice for generating flux maps of the compartmented network of primary metabolism in heterotrophic and mixotrophic plant tissues. While statistically robust protocols for the application of steady-state MFA to plant tissues have been developed by several research groups, the implementation of the method is still far from routine. The effort required to produce a flux map is more than justified by the information that it contains about the metabolic phenotype of the system, but it remains the case that steady-state MFA is both analytically and computationally demanding. This article provides an overview of principles that underpin the implementation of steady-state MFA, focusing on the definition of the metabolic network responsible for redistribution of the label, experimental considerations relating to data collection, the modelling process that allows a set of metabolic fluxes to be deduced from the labelling data, and the interpretation of flux maps. The article draws on published studies of Arabidopsis cell cultures and other systems, including developing oilseeds, with the aim of providing practical guidance and strategies for handling the issues that arise when applying steady-state MFA to the complex metabolic networks encountered in plants.     

Best Practices in Policy and Access (Coding and Reimbursement) for Weight Loss Surgery

To update evidence‐based best practice guidelines for coding and reimbursement and establish policy and access standards for weight loss surgery (WLS). Systematic search of English‐language literature on WLS and health‐care policy, access, insurance reimbursement, coding, private payers, public policy, and mandated benefits published between April 2004 and May 2007 in MEDLINE, EMBASE, and the Cochrane Library. Use of key words to narrow the search for a selective review of abstracts, retrieval of full articles, and grading of evidence according to systems used in established evidence‐based models. We identified 51 publications in our literature search; the 20 most relevant were examined in detail. These included reviews, cost‐benefit analyses, and trend and cost studies from administrative databases. Literature on policy issues surrounding WLS are very sparse and largely focused on economic analyses. Reports on policy initiatives in the public and private arenas are primarily limited to narrative reviews of nonsurgical efforts to fight obesity. A substantial body of work shows that WLS improves or reverses most obesity‐related comorbidities. Mounting evidence also indicates that WLS confers a significant survival advantage for those who undergo it. WLS is a viable and cost‐effective treatment for an increasingly common disease, and policy decisions are more frequently being linked to incentives for national health‐care goals. However, access to WLS often varies by payer and region. Currently, there are no uniform criteria for determining patient appropriateness for surgery.     

Expert Panel on Weight Loss Surgery: Executive Report Update

Rapid shifts in the demographics and techniques of weight loss surgery (WLS) have led to new issues, new data, new concerns, and new challenges. In 2004, this journal published comprehensive evidence‐based guidelines on WLS. In this issue, we've updated those guidelines to assure patient safety in this fast‐changing field. WLS involves a uniquely vulnerable population in need of specialized resources and ongoing multidisciplinary care. Timely best‐practice updates are required to identify new risks, develop strategies to address them, and optimize treatment. Findings in these reports are based on a comprehensive review of the most current literature on WLS; they directly link patient safety to methods for setting evidence‐based guidelines developed from peer‐reviewed scientific publications. Among other outcomes, these reports show that WLS reduces chronic disease risk factors, improves health, and confers a survival benefit on those who undergo it. The literature also shows that laparoscopy has displaced open surgery as the predominant approach; that government agencies and insurers only reimburse procedures performed at accredited WLS centers; that best practice care requires close collaboration between members of a multidisciplinary team; and that new and existing facilities require wide‐ranging changes to accommodate growing numbers of severely obese patients. More than 100 specialists from across the state of Massachusetts and across the many disciplines involved in WLS came together to develop these new standards. We expect them to have far‐reaching effects of the development of health care policy and the practice of WLS.     

Response of cytoplasmic pH to anoxia in plant tissues with altered activities of fermentation enzymes: application of methyl phosphonate as an NMR pH probe

BACKGROUND AND AIMS: Acidification of the cytoplasm is a commonly observed response to oxygen deprivation in plant tissues that are intolerant of anoxia. The response was monitored in plant tissues with altered levels of lactate dehydrogenase (LDH) and pyruvate decarboxylase (PDC) with the aim of assessing the contribution of the targeted enzymes to cytoplasmic pH (pH(cyt)) regulation. METHODS: The pH(cyt) was measured by in vivo (31)P nuclear magnetic resonance (NMR) spectroscopy using methyl phosphonate (MeP) as a pH probe. The potential toxicity of MeP was investigated by analysing its effect on the metabolism of radiolabelled glucose. KEY RESULTS: MeP accumulated to detectable levels in the cytoplasm and vacuole of plant tissues exposed to millimolar concentrations of MeP, and the pH-dependent (31)P NMR signals provided a convenient method for measuring pH(cyt) values in tissues with poorly defined signals from the cytoplasmic inorganic phosphate pool. Pretreatment of potato (Solanum tuberosum) tuber slices with 5 mm MeP for 24 h did not affect the metabolism of [U-(14)C]glucose or the pattern of (14)CO(2) release from specifically labelled [(14)C]-substrates. Time-courses of pH(cyt) measured before, during and after an anoxic episode in potato tuber tissues with reduced activities of LDH, or in tobacco (Nicotiana tabacum) leaves with increased activities of PDC, were indistinguishable from their respective controls. CONCLUSIONS: MeP can be used as a low toxicity (31)P NMR probe for measuring intracellular pH values in plant tissues with altered levels of fermentation enzymes. The measurements on transgenic tobacco leaves suggest that the changes in pH(cyt) during an anoxic episode are not dominated by fermentation processes; while the pH changes in the potato tuber tissue with reduced LDH activity show that the affected isozymes do not influence the anoxic pH response.     

Insights into plant metabolic networks from steady-state metabolic flux analysis

Steady-state metabolic flux analysis (MFA) is an experimental approach that allows the measurement of multiple fluxes in the core network of primary carbon metabolism. It is based on isotopic labelling experiments, and although well established in the analysis of micro-organisms, and some mammalian systems, the extension of the method to plant cells has been challenging because of the extensive subcellular compartmentation of the metabolic network. Despite this difficulty there has been substantial progress in developing robust protocols for the analysis of heterotrophic plant metabolism by steady-state MFA, and flux maps have now been published that reflect the metabolic phenotypes of excised root tips, developing embryos and cotyledons, hairy root cultures, and cell suspensions under a variety of physiological conditions. There has been a steady improvement in the quality, extent and statistical reliability of these analyses, and new information is emerging on the performance of the plant metabolic network and the contributions of specific pathways.