Relationship between isotopic reversibility and futile cycles in isolated rat liver parenchymal cells

Evidence is presented for isotopic flow between glucose and glucose-6P and between fructose-6P and fructose 1,6diP during gluconeogenesis. Inhibitors of glucokinase (glucosamine, 2-deoxyglucose) inhibit the isotopic counterflow. Transaldolase exchange is ruled out by using hexoses labeled in the top half of the molecule.     

On the analysis of futile cycles in metabolism

So-called futile cycles in cellular metabolism consist of paired opposing reactions that, if simultaneously operant, act only to degrade free energy of ATP to heat. Previous considerations of the behavior of such substrate cycles have indicated their possible usefulness in regulating flux along metabolic pathways, but such analyses have treated the cycles in isolation, i.e. without taking into account the effects of enzymatic inputs to and outputs from the cycle. We here develop models of three typical substrate cycles that include enzymatic inputs to and outputs from the cycle and allow the enzymes of the cycles per se to be subject to a variety of allosteric modulations. The non-linear equations which describe these models were solved by an iterative procedure for sets of parameter values of metabolic interest. The results, when analyzed using appropriate definitions of regulatory sensitivity and energetic futility, demonstrate that the effects of the enzymes leading into and out of the cycle may cause profound changes in the operation of the substrate cycle and therefore may not be ignored. We find that the structural differences among the three cycles considered here result in corresponding functional differences. Our results suggest that (1) the fructose-6-P/fructose-1,6-di-P cycle acts effectively to gate bidirectional flux, but doesn't appreciably enhance regulation of unidirectional flux, (2) the glucose/glucose-6-P cycle is well suited to perform a homeostatic function and to adjust the set points for these two metabolites, and (3) the cycle at the pyruvate crossroads functions largely as a complex switch box that directs metabolic flow towards gluconeogenesis or glycolysis not only in response to inputs of or requirements for oxaloacetate, pyruvate, and phosphoenolpyruvate, but also in response to the combined action of allosteric modulators on the individual enzymes of this substrate cycle.     

The role of futile cycles in the energetics of bacterial growth

In this contribution we describe the occurrence of futile cycles in growing bacteria. These cycles are thought to be active when organisms contain two uptake systems for a particular nutrient (one with a high, the other with a low affinity for its substrate). The high-affinity system is responsible for uptake of the nutrient, some of which is subsequently lost to the medium again via leakage through the low-affinity-system. A special futile cycle is caused under some growth conditions by the extremely rapid diffusion of ammonia through bacterial membranes. When the ammonium ion is taken up via active transport, the couple NH3/NH4+ will act as an uncoupler. This is aggravated by the chemical similarity of the potassium and the ammonium ion, which leads to ammonium ion transport via the Kdp potassium transport system when the potassium concentration in the medium is low. Other examples of futile cycles, such as those caused by the production of fatty acids by fermentation, are briefly discussed.     

Acetate metabolism in Escherichia coli strains lacking phosphoenolpyruvate: carbohydrate phosphotransferase system; evidence of carbon recycling strategies and futile cycles

The ptsHIcrr operon was deleted from Escherichia coli wild-type JM101 to generate strain PB11 (PTS(-)). In a mutant derived from PB11 that partially recovered its growth capacity on glucose by an adaptive evolution process (PB12, PTS(-)Glc(+)), part of the phosphoenolpyruvate not used in glucose transport has been utilized for the synthesis of aromatic compounds. In this report, it is shown that on acetate as a carbon source, PB11 displayed a specific growth rate (mu) higher than PB12 (0.21 and 0.13 h(-1), respectively) while JM101 had a mu of 0.28 h(-1). To understand these growth differences on acetate, we compared the expression profiles of central metabolic genes by RT-PCR analysis. Obtained data revealed that some gluconeogenic genes were downregulated in both PTS(-) strains as compared to JM101, while most glycolytic genes were upregulated in PB12 in contrast to PB11 and JM101. Furthermore, inactivation of gluconeogenic genes, like ppsA, sfcA, and maeB,and poxB gene that codes for pyruvate oxidase, has differential impacts in the acetate metabolism of these strains. Results indicate that growth differences on acetate in the PTS(-) derivatives are due to potential carbon recycling strategies, mainly in PB11, and futile carbon cycles, especially in PB12.     

Isotopic evidence for age-related immigration to imperial Rome

Oxygen stable isotope ratios (delta(18)O) have been determined in carbonate in paired first and third molar teeth from individuals (N = 61) who lived in the town of Portus Romae ("Portus") and who were buried in the necropolis of Isola Sacra (First to Third centuries AD) near Rome, Italy. We compare these analyses with data for deciduous teeth of modern Roman children. Approximately one-third of the archaeological sample has first molar (M1) values outside the modern range, implying a large rate of population turnover at that time, consistent with historical data. Delta (18)O(ap) values suggest that a group within the sample migrated to the area before the third molar (M3) crown had completely formed (i.e., between 10 and 17.5 years of age). This is the first quantitative assessment of population mobility in Classical antiquity. This study demonstrates that migration was not limited to predominantly single adult males, as suggested by historical sources, but rather a complex phenomenon involving families. We hypothesize that migrants most likely came from higher elevations to the East and North of Rome. One individual with a higher delta(18)O value may have come (as a child) from an area isotopically similar to North Africa.     

Futile cycles in isolated perfused rat liver and in isolated rat liver parenchymal cells.

Isolated livers from fed rats were perfused with a medium containing glucose labeled uniformly with ¹⁴C and specifically with ³H. There was considerable formation of glucose from endogenous sources but simultaneously uptake of about half of the ¹⁴C in glucose. After 2 hours the ${}^3\text{H}{}^{14}\text{C}$ ratios in perfusate glucose decreased by 55–60% with (2-³H, U-¹⁴C), 40–50% with (5-³H, U-¹⁴C), 25–30% with (3-³H or 4-³H, U-¹⁴C) and by 10–15% with (6-³H, U-¹⁴C) glucose. Qualitatively comparable patterns were obtained with rat hepatocytes. These results demonstrate recycling of carbon between glucose and pyruvate. Superimposed upon this there is an extensive futile cycle between glucose and glucose 6-P. There is also futile cycling between fructose 6-P and fructose 1,6 P₂ and to a small extent between phosphoenol pyruvate and pyruvate.     

Metabolic futile cycles and their functions: a systems analysis of energy and control

It has long been hypothesised that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, a quantitative theory was developed for this idea based on open-system thermodynamics and metabolic control analysis. It is shown that the stoichiometric sensitivity of an intermediary metabolite concentration with respect to changes in steady-state flux is governed by the effective equilibrium constant of the intermediate formation, and the equilibrium can be regulated by a futile cycle. The direction of the shift in the effective equilibrium constant depends on the direction of operation of the futile cycle. High stoichiometric sensitivity corresponds to ultrasensitivity of an intermediate concentration to net flow through a pathway; low stoichiometric sensitivity corresponds to super-robustness of concentration with respect to changes in flux. Both cases potentially play important roles in metabolic regulation. Futile cycles actively shift the effective equilibrium by expending energy; the magnitude of changes in effective equilibria and sensitivities is a function of the amount of energy used by a futile cycle. This proposed mechanism for control by futile cycles works remarkably similar to kinetic proofreading in biosynthesis. The sensitivity of the system is also intimately related to the rate of concentration fluctuations of intermediate metabolites. The possibility of different roles for the two major mechanisms within cellular biochemical regulation, namely reversible chemical modifications via futile cycles and shifting equilibrium by macromolecular binding, are discussed.     

Isotopic labeling of DNA in rat adipose tissue: evidence for proliferating cells associated with mature adipocytes.

The intraperitoneal administration of [3H]thymidine to adult rats resulted in the rapid appearance of label in the adipocyte fraction of collagenase digests of adipose tissue. Low-speed centrifugation followed by freezing and slicing showed the label to be uniformly distributed in the adipocyte fraction. The presence of label in DNA was confirmed by hydrolysis with deoxyribonuclease and by inhibition of incorporation with hydroxyurea. Organelle fractionation revealed that the label was predominantly in nuclei, and radioautography showed that only a few adipocyte nuclei were labeled. The label in the adipocyte fraction could not be reduced by increased collagenase digestion or by trypsin treatment. Mixing of labeled adipocytes with unlabeled stroma did not result in decrease of label and addition of labeled stroma to unlabeled adipocytes did not cause significant transfer of radioactivity. Addition of [3H]thymidine to the collagenase digestion medium of unlabeled adipose tissue resulted in more incorporation by adipocytes than by stroma, suggesting the presence of a very rapidly proliferating cell type associated more with adipocytes than with stroma. In vivo turnover studies of labeled DNA indicated that there are two components in both adipocytes and stroma, a rapidly labeled component with a half-life of only several days and another with a half-life of several months. These experiments suggest that there is a rapidly proliferating cell type in adipose tissue, closely associated with mature adipocytes, that may be an adipocyte progenitor or may have some other unknown function.     

Isotopic evidence of unaccounted for Fe and Cu erythropoietic pathways

Despite its potential importance for understanding perturbations in the Fe-Cu homeostatic pathways, the natural isotopic variability of these metals in the human body remains unexplored. We measured the Fe, Cu, and Zn isotope compositions of total blood, serum, and red blood cells of ~50 young blood donors by multiple-collector ICP-MS after separation and purification by anion exchange chromatography. Zinc shows much less overall isotopic variability than Fe and Cu, which indicates that isotope fractionation depends more on redox conditions than on ligand coordination. On average, Fe in erythrocytes is isotopically light with respect to serum, whereas Cu is heavy. Iron and Cu isotope compositions clearly separate erythrocytes of men and women. Fe and Cu from B-type men erythrocytes are visibly more fractionated than all the other blood types. Isotope compositions provide an original method for evaluating metal mass balance and homeostasis. Natural isotope variability shows that the current models of Fe and Cu erythropoiesis violate mass balance requirements. It unveils unsuspected major pathways for Fe, with erythropoietic production of isotopically heavy ferritin and hemosiderin, and for Cu, with isotopically light Cu being largely channeled into blood and lymphatic circulation rather than into superoxide dismutase-laden erythrocytes. Iron isotopes provide an intrinsic measuring rod of the erythropoietic yield, while Cu isotopes seem to gauge the relative activity of erythropoiesis and lymphatics.     

Isotopic evidence for methane-based chemosynthesis in the Upper Floridan aquifer food web

Anecdotal observations of the Dougherty plain cave crayfish (Cambarus cryptodytes), the Georgia blind cave salamander (Haideotriton wallacei), and albinistic isopods (Caecidotea sp.) at great depths below the land surface and distant from river corridors suggest that obligate aquifer-dwelling (troglobitic) organisms are widely distributed throughout the limestone Upper Floridan aquifer (UFA). One mechanism by which subterranean life can proliferate in an environment void of plant productivity is through a microbial food web that includes chemosynthesis. We examined this possibility in the UFA by measuring the isotopic composition (¹³C, ¹⁴C, and ¹⁵N) of tissues from troglobitic macrofauna. Organisms that were captured by cave divers entering into spring conduits had δ¹³C values that suggested plant matter as a primary food resource (cave crayfish, –24.6 ± 2.7‰, n = 9). In contrast, δ¹³C values were significantly depleted in organisms retrieved from wells drilled into areas of the UFA remote from spring and sinkhole conduits (cave crayfish −34.7 ± 9.8‰, n = 10). Depleted ¹³C values in crayfish were correlated with radiocarbon (Δ¹⁴C) depletion relative to modern values. The results suggest that methane-based microbial chemosynthetic pathways support organisms living in the remote interior of the aquifer, at least in part.     

Sources of thymidine and analogs fueling futile damage-repair cycles and ss-gap accumulation during thymine starvation in Escherichia coli

Thymine deprivation in thyA mutant E. coli causes thymineless death (TLD) and is the mode of action of popular antibacterial and anticancer drugs, yet the mechanisms of TLD are still unclear. TLD comprises three defined phases: resistance, rapid exponential death (RED) and survival, with the nature of the resistance phase and of the transition to the RED phase holding key to TLD pathology. We propose that a limited source of endogenous thymine maintains replication forks through the resistance phase. When this source ends, forks undergo futile break-repair cycle during the RED phase, eventually rendering the chromosome non-functional. Two obvious sources of the endogenous thymine are degradation of broken chromosomal DNA and recruitment of thymine from stable RNA. However, mutants that cannot degrade broken chromosomal DNA or lack ribo-thymine, instead of shortening the resistance phase, deepen the RED phase, meaning that only a small fraction of T-starved cells tap into these sources. Interestingly, the substantial chromosomal DNA accumulation during the resistance phase is negated during the RED phase, suggesting futile cycle of incorporation and excision of wrong nucleotides. We tested incorporation of dU or rU, finding some evidence for both, but DNA-dU incorporation accelerates TLD only when intracellular [dUTP] is increased by the dut mutation. In the dut ung mutant, with increased DNA-dU incorporation and no DNA-dU excision, replication is in fact rescued even without dT, but TLD still occurs, suggesting different mechanisms. Finally, we found that continuous DNA synthesis during thymine starvation makes chromosomal DNA increasingly single-stranded, and even the dut ung defect does not completely block this ss-gap accumulation. We propose that instability of single-strand gaps underlies the pathology of thymine starvation.     

Southern French Neolithic populations: Isotopic evidence for regional specificities in environment and diet

The Middle Neolithic of the Northwestern Mediterranean area (～4500–3500 BC cal) is characterized by the development of food production techniques as well as by increasing social complexity. These characteristics could have had an impact on human dietary patterns. To evaluate human dietary practices and lifeways of the Middle Neolithic populations from the South of France, stable carbon and nitrogen isotope analysis was carried out on 57 human and 53 faunal bones from seven archaeological sites located in the Languedoc and Garonne regions between 20 and 100 km from the Mediterranean Sea, respectively. Results show regional differences in carbon isotope values. Animal and human bones from the Languedoc region are significantly enriched in ¹³C relative to the Garonne. Conversely, human and dog bones from the Garonne region are significantly enriched in ¹⁵N compared to human and dog bones from the Languedoc region. These results highlight the importance of the local ecosystem in human and animal diet as well as a regional differentiation of palaeodietary behavior, which probably relates to economic and social factors. The comparison of stable isotope data with archaeological and biological evidence does not show any significant intra‐ or interpopulation differences. However, the presence of human outliers suggests that migration probably occurred, perhaps in relation to the trade of animals and/or materials. This study also highlights the importance of investigating local animal stable isotope values for the interpretation of human palaeodiet. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Isotopic evidence of partial mycoheterotrophy in Burmannia coelestis (Burmanniaceae)

The Burmanniaceae contain several lineages of achlorophyllous mycoheterotrophic plants that associate with arbuscular mycorrhizal fungi (AMF). Here we investigate the isotopic profile of a green and potentially mycoheterotrophic plant in situ, Burmannia coelestis, and associated reference plants. We generated δ ¹³C and δ ¹⁵N stable isotope profiles for five populations of B. coelestis. Burmannia coelestis was significantly enriched in ¹³C relative to surrounding C₃ reference plants and significantly depleted in ¹³C relative to C₄ reference plants. No significant differences were detected in ¹⁵N enrichment between B. coelestis and reference plants. The isotopic profiles measured are suggestive of partial mycoheterotrophy in B. coelestis. Within the genus Burmannia transitions to full mycoheterotrophy have occurred numerous times, suggesting that some green Burmannia species are likely to be partially mycoheterotrophic but in many conditions this mode of nutrition may only be detectable using natural abundance stable isotopic methods, such as when associated with C₄ mycorrhizal plants.     

Isotopic evidence for endogenous protein contributions to greylag goose Anser anser flight feathers

Feather stable isotope composition may not reflect local isoscapes in which they were grown if supplemented with protein of endogenous origin. Thus, feather isotope analysis, combined with knowledge of local isoscapes can be used to infer endogenous nutrient composition to feathers in cases where birds travel to moult. We investigated this possibility in a study of flightless moulting greylag geese Anser anser on the Danish island of Saltholm, which are known to mobilise endogenous protein stores (acquired at previous terrestrial staging locations in Sweden) to reconstitute muscle blocks and organs whilst feeding on a saltmarsh (i.e. marine-influenced) diet with contrasting stable isotope ratios. We used stable isotope (δ¹³C, δ¹⁵N) measurements to test the prediction that new-grown flight feathers would have stable isotope values intermediate between those derived from a purely terrestrial C₃ diet and one composed purely of saltmarsh plants. Feather δ¹³C and δ¹⁵N values were intermediate between those expected for feather material derived from local saltmarsh (i.e. exogenous) food items and Swedish terrestrial (endogenous muscle) sources, suggesting a mixing of endogenous and exogenous sources. These results confirm that moult migrant Anatidae exploit body stores to meet specific protein needs during the flightless period of remige regrowth and caution against the use of feather stable isotope ratios as direct indicators of the isotopic environment in which they were regrown, where endogenous contributions may occur.     

Isotopic evidence for the occurrence of biological nitrification and nitrogen deposition processing in forest canopies

This study examines the role of tree canopies in processing atmospheric nitrogen (N_dep) for four forests in the United Kingdom subjected to different N_dep: Scots pine and beech stands under high N_dep (HN, 13–19 kg N ha^?1 yr^?1), compared to Scots pine and beech stands under low N_dep (LN, 9 kg N ha^?1 yr^?1). Changes of NO₃‐N and NH₄‐N concentrations in rainfall (RF) and throughfall (TF) together with a quadruple isotope approach, which combines δ¹⁸O, Δ¹⁷O and δ¹⁵N in NO₃^? and δ¹⁵N in NH₄⁺, were used to assess N transformations by the canopies. Generally, HN sites showed higher NH₄‐N and NO₃‐N concentrations in RF compared to the LN sites. Similar values of δ¹⁵N‐NO₃^? and δ¹⁸O in RF suggested similar source of atmospheric NO₃^? (i.e. local traffic), while more positive values for δ¹⁵N‐NH₄⁺ at HN compared to LN likely reflected the contribution of dry NH_x deposition from intensive local farming. The isotopic signatures of the N‐forms changed after interacting with tree canopies. Indeed, ¹⁵N‐enriched NH₄⁺ in TF compared to RF at all sites suggested that canopies played an important role in buffering dry N_dep also at the low N_dep site. Using two independent methods, based on δ¹⁸O and Δ¹⁷O, we quantified for the first time the proportion of NO₃^? in TF, which derived from nitrification occurring in tree canopies at the HN site. Specifically, for Scots pine, all the considered isotope approaches detected biological nitrification. By contrast for the beech, only using the mixing model with Δ¹⁷O, we were able to depict the occurrence of nitrification within canopies. Our study suggests that tree canopies play an active role in the N cycling within forest ecosystems. Processing of N_dep within canopies should not be neglected and needs further exploration, with the combination of multiple isotope tracers, with particular reference to Δ¹⁷O.     

Little evidence for a major role of Ca2+ in cold-induced injury of liver cells

We have previously shown that cold-induced injury to hepatocytes and liver endothelial cells occurs predominantly via an iron-dependent pathway. However, other groups have reported evidences suggesting that Ca²⁺ ions could be involved in the process of cold-induced injury of liver cells. We here assessed the relative importance and potential interaction of both pathways in cultured primary hepatocytes and cultured liver endothelial cells. The sequence cold incubation/rewarming of hepatocytes and endothelial cells led to an increase in the cytosolic calcium concentration during the early rewarming phase, but the increased cytosolic calcium concentration did not correlate with cell injury. A partial protection from cold-induced cell injury was achieved by the intracellular calcium chelators Quin-2 and BAPTA. However, additional experiments showed that the ability of these chelators to bind iron was probably responsible for a major part of this protection. Incubation in calcium-free media led to an increased cell injury and a physiological calcium concentration (2.5 mM) was protective. In addition, targeting suggested downstream pathways of calcium-dependent cold-induced injury, i.e. by the addition of Ruthenium Red, an inhibitor of mitochondrial Ca²⁺ uniporter, or by inhibiting Bax translocation to the mitochondria, did not provide protection from cold-induced injury in both cell types. Taken together, our data suggest that calcium increases but does not play a major role in cold-induced cell injury to hepatocytes and liver endothelial cells.     

Isotopic evidence of arbuscular mycorrhizal cheating in a grassland gentian species

All orchids and pyroloids are mycoheterotrophic at least in the early stage. Many species are predisposed to mycoheterotrophic nutrition even in the adult     

Trans‐Atlantic slavery: Isotopic evidence for forced migration to Barbados

The question of the ultimate origin of African slaves is one of the most perplexing in the history of trans‐Atlantic slavery. Here we present the results of a small, preliminary isotopic study that was conducted in order to determine the geographical origin of 25 enslaved Africans who were buried at the Newton plantation, Barbados, sometime between the late 17th and early 19th century. In order to gain a more nuanced understanding of the slaves' origin, we used a combination of carbon, nitrogen, oxygen, and strontium isotope analyses. Carbon and nitrogen isotope ratios were determined in bone and dentinal collagen; oxygen and strontium isotopes were measured in tooth enamel. Results suggest that the majority of individuals were born on the island, if not the estate itself. Seven individuals, however, yielded enamel oxygen and strontium ratios that are inconsistent with a Barbadian origin, which strongly suggests that we are dealing with first‐generation captives who were brought to the island with the slave trade. This idea is also supported by the fact that their carbon and nitrogen stable isotope values differ markedly between their teeth and bones. These intra‐skeletal shifts reflect major dietary changes that probably coincided with their enslavement and forced migration to Barbados. While it is impossible to determine their exact origins, the results clearly demonstrate that the slaves did not all grow up in the same part of Africa. Instead, the data seem to suggest that they originated from at least three different areas, possibly including the Gold Coast and the Senegambia. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.