Poly(ADP-ribosyl)ation of chromatin in an in-vitro poly(ADP-ribose)-turnover system.

This paper describes the effect of an in-vitro poly(ADP-ribose) turnover system on the poly(ADP-ribosyl)ation of chromatin. Both poly(ADP-ribose)polymerase and poly(ADP-ribose)glycohydrolase were highly purified and used in 4 different turnover systems: non-turnover, slow, medium and fast turnover. These turnover systems were designed to reflect possible turnover conditions in intact cells. The major protein acceptors for poly(ADP-ribose) are histones and the polymerase itself, a process referred to as automodification. The level of poly(ADP-ribose) modification of polymerase, histone H1 and core histones has been measured. The size of the polymer for each of the 3 groups of acceptor proteins has been determined by gel electrophoresis. After many turnover cycles at medium and fast turnover, the histones (H1 and core) become the main poly(ADP-ribose) acceptor proteins. The rate at which steady-state polymer levels are reached and the total accumulation of polymer in a given turnover system are both inversely proportional to the amount of glycohydrolase present. Furthermore, increasing amounts of glycohydrolase in the turnover systems reduces average polymer size. The polymer synthesized in the medium and fast turnover systems is degraded by glycohydrolase in a biphasic fashion and in these systems the half-life of polymer agreed with results found in intact cells. Our results show that the relative levels of polymerase and glycohydrolase activities can regulate the proportional poly(ADP-ribose) distribution on chromatin-associated acceptor proteins during steady-state turnover conditions. The patterns of modification of polymerase and histones under turnover conditions agree with in vivo observations.     

森林生态系统细根周转规律及影响因素

根系周转是陆地生态系统碳循环的关键过程, 对研究土壤碳库变化及全球气候变化均具有重要意义。然而由于根系周转率的测量计算方法较多, 不同方法得出的结果差异较大, 且目前对全球区域尺度上森林生态系统根系周转的研究还不够充分, 使得全球森林生态系统根系周转变化规律仍不清楚。该研究通过收集文献数据并统一周转率计算方法, 对全球5种森林类型的细根周转空间格局进行整合, 同时结合土壤理化性质和气候数据, 得出影响森林生态系统细根周转的因子。结果表明, 不同森林类型细根周转率存在显著差异, 且随着纬度的升高逐渐降低; 森林生态系统细根周转率与年平均温度和年平均降水量呈正相关; 森林生态系统细根周转率与土壤有机碳含量呈正相关但与土壤pH值呈负相关。该研究为揭示森林生态系统细根周转规律及机制提供了科学依据。     

Regulation of Bacterial Cell Walls: Turnover of Cell Wall in Staphylococcus aureus

The cell wall of Staphylococcus aureus was shown to undergo turnover during exponential growth. The rate of turnover, about 15% per generation, was identical for both cell wall polymers, peptidoglycan and teichoic acid. Both the old and newly synthesized wall material appeared to undergo turnover at similar rates. The rate of turnover followed first-order kinetics until more than 90% of the original wall was lost. Cell wall turnover was completely blocked under conditions of unbalanced synthesis known to inhibit cellular autolysis, e.g., addition of chloramphenicol. Cell wall turnover was shown to occur in a number of different strains of S. aureus and appears to be widely distributed in this species.     

Regulation of mitochondrial protein turnover by thyroid hormone(s)

1. The effect of thyroidectomy on turnover rates of liver, kidney and brain mitochondrial proteins was examined. 2. In the euthyroid state, liver and kidney mitochondria show a synchronous turnover with all protein components showing more or less identical half-lives compared with the whole mitochondria. The brain mitochondrial proteins show asynchronous turnover, the soluble proteins having shorter half-lives. 3. Mitochondrial DNA (m-DNA) of liver and kidney has half-lives comparable with that of whole mitochondria from these tissues. 4. Thyroidectomy results in increased half-lives of liver and kidney mitochondria, with no apparent change in the half-life of brain mitochondria. 5. A detailed investigation of the turnover rates of several protein components revealed a significant decrease in the turnover rates of mitochondrial insoluble proteins from the three tissues under study. 6. The turnover rates of m-DNA of liver and kidney show a parallel decrease. 7. Thus it is apparent that thyroid hormone(s) may have a regulatory role in maintaining the synchrony of turnover of liver and kidney mitochondria in the euthyroid state. Turnover of brain mitochondria may perhaps be regulated by some other factor(s) in addition to thyroid hormone(s). 8. It seems likely that during mitochondrial turnover m-DNA and insoluble proteins may constitute a major unit. 9. The mitochondrial protein contents of the three tissues are not affected by thyroidectomy. 10. No correlation was seen between the turnover rate of mitochondria and cathepsin activity in any of the tissues under study in normal or thyroidectomized animals. 11. On the other hand, mitochondrial proteinase activity shows good correlation with the turnover rates of mitochondria in normal animals, and a parallel decrease in activity comparable with the decreased rates of turnover is observed after thyroidectomy. 12. It is concluded that mitochondrial proteinase activity may play a significant role in their protein turnover.     

Antigen-driven T-cell turnover

A mathematical model is developed to characterize the distribution of cell turnover rates within a population of T lymphocytes. Previous models of T-cell dynamics have assumed a constant uniform turnover rate; here we consider turnover in a cell pool subject to clonal proliferation in response to diverse and repeated antigenic stimulation. A basic framework is defined for T-cell proliferation in response to antigen, which explicitly describes the cell cycle during antigenic stimulation and subsequent cell division. The distribution of T-cell turnover rates is then calculated based on the history of random exposures to antigens. This distribution is found to be bimodal, with peaks in cell frequencies in the slow turnover (quiescent) and rapid turnover (activated) states. This distribution can be used to calculate the overall turnover for the cell pool, as well as individual contributions to turnover from quiescent and activated cells. The impact of heterogeneous turnover on the dynamics of CD4(+) T-cell infection by HIV is explored. We show that our model can resolve the paradox of high levels of viral replication occurring while only a small fraction of cells are infected.     

Actin turnover is required to prevent axon retraction driven by endogenous actomyosin contractility

Growth cone motility and guidance depend on the dynamic reorganization of filamentous actin (F-actin). In the growth cone, F-actin undergoes turnover, which is the exchange of actin subunits from existing filaments. However, the function of F-actin turnover is not clear. We used jasplakinolide (jasp), a cell-permeable macrocyclic peptide that inhibits F-actin turnover, to study the role of F-actin turnover in axon extension. Treatment with jasp caused axon retraction, demonstrating that axon extension requires F-actin turnover. The retraction of axons in response to the inhibition of F-actin turnover was dependent on myosin activity and regulated by RhoA and myosin light chain kinase. Significantly, the endogenous myosin-based contractility was sufficient to cause axon retraction, because jasp did not alter myosin activity. Based on these observations, we asked whether guidance cues that cause axon retraction (ephrin-A2) inhibit F-actin turnover. Axon retraction in response to ephrin-A2 correlated with decreased F-actin turnover and required RhoA activity. These observations demonstrate that axon extension depends on an interaction between endogenous myosin-driven contractility and F-actin turnover, and that guidance cues that cause axon retraction inhibit F-actin turnover.     

Patterns of species richness and turnover along the pH gradient in deciduous forests: testing the continuum hypothesis

Question: (i) How do species richness and species turnover change along a pH gradient? (ii) What are possible driving factors behind these patterns? (iii) Can the observed patterns be explained by an individualistic continuum concept that postulates independence of species responses and constant turnover rates? Location: Semi‐natural, deciduous hardwood forests in NW Germany (558 plots). Methods: The instantaneous rate of compositional turnover is measured by the sum of slope angles of modelled response curves (119 understorey species) at any point along the pH gradient. Total turnover rate, positive turnover rate (species increasing in probability of occurrence) and negative turnover rate (species decreasing in probability of occurrence) are calculated separately. Species richness is modelled using Poisson regression and by calculating the sum of predicted probabilities at any gradient point. Turnover rates are compared with those calculated from a null model based on a Gaussian community model. Soil chemical analyses of 49 plots are used to interpret biodiversity patterns. Results: Species richness shows a hump‐shaped relation to pH(CaCl₂) with a minor decline at approximately pH>5.0. The decline is possibly due to the confounding influence of water regime and local species pool effects. Increasing richness from pH 2.5 to 4.7 can be traced back to positive turnover exceeding negative turnover. Peaks in turnover rates, dominated by positive turnover, are located at pH 3.7 and 2.8, where turnover rates considerably exceed rates derived from the null model. The turnover pattern can be related to soil chemical conditions, e.g. decreasing base saturation, Al and H⁺ toxicity and the occurrence of mor. Conclusions: The high turnover rates and the massive imbalance in positive and negative turnover rates found in deciduous forests cannot be explained by the individualistic continuum concept. Physiological constraints at the gradient limits and species pool effects could be responsible for this. Their role should be considered more explicitly in vegetation concepts dealing with the continuum‐discontinuum controversy. The presented approach can be regarded as a comprehensive analytical tool for a better understanding of biodiversity patterns along environmental gradients by linking species richness, turnover and response curve types.     

Dual pathways for ribonucleic acid turnover in WI-38 but not in I-cell human diploid fibroblasts.

The turnover rates of 3H-labeled 18S ribosomal ribonucleic acid (RNA), 28S ribosomal RNA, transfer RNA, and total cytoplasmic RNA were very similar in growing WI-38 diploid fibroblasts. The rate of turnover was at least twofold greater when cell growth stopped due to cell confluence, 3H irradiation, or treatment with 20 mM NaN3 or 2 mM NaF. In contrast, the rate of total 3H-protein turnover was the same in growing and nongrowing cells. Both RNA and protein turnovers were accelerated at least twofold in WI-38 cells deprived of serum, and this increase in turnover was inhibited by NH4Cl. These results are consistent with two pathways for RNA turnover, one of them being nonlysosomal and the other being lysosome mediated (NH4Cl sensitive), as has been suggested for protein turnover. Also consistent with the notion of two pathways for RNA turnover were findings with I-cells, which are deficient for many lysosomal enzymes, and in which all RNA turnover was nonlysosomal (NH4Cl resistant).     

Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover

The turnover of each protein in the mammalian proteome is a functionally important characteristic. Here, we employed high-resolution mass spectrometry to quantify protein dynamics in nondividing mammalian cells. The ratio of externally supplied versus endogenous amino acids to de novo protein synthesis was about 17:1. Using subsaturating SILAC labeling, we obtained accurate turnover rates of 4106 proteins in HeLa and 3528 proteins in C2C12 cells. Comparison of these human and mouse cell lines revealed a highly significant turnover correlation of protein orthologs and thus high species conservation. Functionally, we observed statistically significant trends for the turnover of phosphoproteins and gene ontology categories that showed extensive covariation between mouse and human. Likewise, the members of some protein complexes, such as the proteasome, have highly similar turnover rates. The high species conservation and the low complex variances thus imply great regulatory fine-tuning of protein turnover.     

Comparative Proteome Analysis of hAT-MSCs Isolated from Chronic Renal Failure Patients with Differences in Their Bone Turnover Status

The relationship between the stem cells and the bone turnover in uremic bone disease due to chronic renal failure (CRF) is not described. The aim of this study was to investigate the effect of bone turnover status on stem cell properties. To search for the presence of such link and shed some light on stem-cell relevant mechanisms of bone turnover, we carried out a study with mesenchymal stem cells. Tissue biopsies were taken from the abdominal subcutaneous adipose tissue of a CRF patient with secondary hyperparathyroidism with the high turnover bone disease. This patient underwent parathyroidectomy operation (PTX) and another sample was taken from this patient after PTX. A CRF patient with adynamic bone disease with low turnover and a healthy control were also included. Mesenchymal stem cells isolated from the subjects were analyzed using proteomic and molecular approaches. Except ALP activity, the bone turnover status did not affect common stem cell properties. However, detailed proteome analysis revealed the presence of regulated protein spots. A total of 32 protein spots were identified following 2D gel electrophoresis and MALDI-TOF/TOF analyzes. The identified proteins were classified into seven distinct groups and their potential relationship to bone turnover were discussed. Distinct protein expression patterns emerged in relation to the bone turnover status indicate a possible link between the stem cells and bone turnover in uremic bone disease due to CRF.     

Spatial modelling of species turnover identifies climate ecotones,climate change tipping points and vulnerable taxonomic groups

There is an expectation that climate change will drive turnover in the composition of ecological communities. Established methods for predicting the degree of turnover and spatial areas and taxonomic groups that will be most affected from real data are lacking. We tested a combination of spatial modelling tools to make these predictions. Using data from systematic vegetation survey plots from the Adelaide Geosyncline region, southern Australia, we modelled species turnover as a function of bioclimatic and geographic distances and predicted turnover using future climate change scenarios for 2030 and 2070. We conducted bioclimatic gradient analysis (CCA) on species composition data and mapped zones of higher turnover. The method for detecting these zones was tested using a simulation of continuous turnover. A phylogeny was generated for recorded species and correlations of occurrences of phylogenetic groups with species turnover were calculated. Significant turnover was predicted for the least severe climate change scenarios and near‐complete species turnover for the most severe scenario. Gradient analysis revealed discrete transitional zones with more rapid turnover, which were interpreted as a mesic–arid ecotone. Turnover occurred at family level and with increasing temperature and decreasing rainfall there was a shift from the prevalence of Ericaceae, Myrtaceae, Haloragaceae, Cyperaceae, and Xanthorrhoeaceae to that of Amaranthaceae, Malvaceae, Scrophulariaceae, Sapindaceae, and Solanaceae. The mesic end of this climate gradient had relatively low rates of turnover and was interpreted as a refugium with a tipping point. The translation of spatial patterns to temporal change is dependent partly upon scales at which community assembly processes operate and predicts relative vulnerability, but not rates of change, which can only be measured through monitoring. The approach can be applied at any spatial or taxonomic scale subject to sufficient data resolution and can inform management decisions as to biases in climate change risks.     

Metabolic turnover of myelin glycerophospholipids

The apparent half life for metabolic turnover of glycerophospholipids in the myelin sheath, as determined by measuring the rate of loss of label in a myelin glycerophospholipid following radioactive precursor injection, varies with the radioactive precursor used, age of animal, and time after injection during which metabolic turnover is studied. Experimental strategies for resolving apparent inconsistencies consequent to these variables are discussed. Illustrative data concerning turnover of phosphatidylcholine (PC) in myelin of rat brain are presented. PC of the myelin membrane exhibits heterogeneity with respect to metabolic turnover rates. There are at least two metabolic pools of PC in myelin, one with a half life of the order of days, and another with a half life of the order of weeks. To a significant extent biphasic turnover is due to differential turnover of individual molecular species (which differ in acyl chain composition). The two predominant molecular species of myelin PC turnover at very different rates (16:0, 18:1 PC turning over several times more rapidly than 18:0, 18:1 PC). Therefore, within the same membrane, individual molecular species of a phospholipid class are metabolized at different rates. Possible mechanisms for differential turnover of molecular species are discussed, as are other factors that may contribute to a multiphasic turnover of glycerophospholipids.Special issue dedicated to Dr. Marjorie Lees.     

Handling of water and dietary monovalent ions by the young turkey

Sodium and water turnover rates were measured in young turkeys fed diets with three concentrations of NaCl and kept at 12, 18 or 30 degrees C. Sodium absorption averaged approximately 60% and was unaffected by temperature. Water and sodium pools were affected by temperature and sodium intake. Water turnover was linear to sodium turnover at the lower two temperatures. No significant relationship was apparent in birds kept at 30 degrees C. The reciprocal of the slope of the function of water turnover on sodium turnover was 125-170 mM, suggesting an increase in isotonic urine excretion with sodium intake and a corresponding increase in water intake. Dietary sodium and potassium stimulated water turnover similarly. Dietary chloride concentration did not affect water turnover. In the turkey plasma pH and pCO2 were unaffected by a wide range of the anion-cation balance. It is concluded that excess sodium or potassium intakes is handled effectively in the turkey by increased water intake and excretion.     

Quantifying High Resolution Transitional Breaks in Plant and Mammal Distributions at Regional Extent and Their Association with Climate,Topography and Geology

Objectives

We quantify spatial turnover in communities of 1939 plant and 59 mammal species at 2.5 km resolution across a topographically heterogeneous region in south-eastern Australia to identify distributional breaks and low turnover zones where multiple species distributions overlap. Environmental turnover is measured to determine how climate, topography and geology influence biotic turnover differently across a variety of biogeographic breaks and overlaps. We identify the genera driving turnover and confirm the versatility of this approach across spatial scales and locations.

Methods

Directional moving window analyses, rotated through 360°, were used to measure spatial turnover variation in different directions between gridded cells containing georeferenced plant and mammal occurrences and environmental variables. Generalised linear models were used to compare taxic turnover results with equivalent analyses for geology, regolith weathering, elevation, slope, solar radiation, annual precipitation and annual mean temperature, both uniformly across the entire study area and by stratifying it into zones of high and low turnover. Identified breaks and transitions were compared to a conservation bioregionalisation framework widely used in Australia.

Results/Significance

Detailed delineations of plant and mammal turnover zones with gradational boundaries denoted subtle variation in species assemblages. Turnover patterns often diverged from bioregion boundaries, though plant turnover adhered most closely. A prominent break zone contained either comparable or greater numbers of unique genera than adjacent overlaps, but these were concentrated in a small subsection relatively under-protected by conservation reserves. The environmental correlates of biotic turnover varied for different turnover zones in different subsections of the study area. Topography and temperature showed much stronger relationships with plant turnover in a topographically complex overlap, relative to a lowland overlap where weathering was most predictive. This method can quantify transitional turnover patterns from small to broad extents, at different resolutions for any location, and complements broad-scale bioregionalisation schemes in conservation planning.     

CONTROL OF MITOCHONDRIAL TURNOVER UNDER THE INFLUENCE OF THYROID HORMONE

The effect of thyroid hormone on the turnover of mitochondrial DNA and protein was studied in rat heart and liver. Changes in turnover were observed in both thyroidectomized and normal rats following administration of thyroid hormone. In heart and liver the turnover of mitochondrial DNA and protein was slower in thyroidectomized rats than in normal rats. The turnover of mitochondrial DNA and protein was affected similarly following the administration of thyroid hormone, suggesting that mechanisms which control turnover of mitochondrial constituents may be predicated upon a major part of the mitochondrion. In heart a decreased rate of degradation contributes to the increase in total mitochondrial protein. Mitochondrial DNA, labeled before administration of thyroid hormone, turns over, after the start of thyroid hormone administration, at a different rate from that in newly synthesized DNA. The different turnover rates suggest that in liver the pre-existing population of mitochondria is being replaced by another population synthesized under new physiological conditions.     

Determination of cholesterol turnover rate by a one-and two-pool kinetic analysis.

The cholesterol turnover rate in rabbits with alimentary cholesterol atherosclerosis and in guinea-pigs with chronic vitamin C deficiency was studied by a one- and two-pool kinetic analysis. The one-pool analysis yielded exaggeraged values for the turnover rate, but the turnover rate differences between the control and experimental groups in the one- and the two-pool analysis were very similar. One-pool analysis can be used in initial studies to obtain preliminary data on the effect of nutritional, pharmacological and other factors on cholesterol turnover rate.     

Interleukin-2- and phytohemagglutinin-activated proliferation of human T-lymphocytes is accompanied by stimulation of phosphoinositide turnover

Interleukin-2 (IL-2) was more effective than phytohemagglutinin (PHA) in increasing the proliferative activity of human T-lymphocytes. Unlike PHA, IL-2 stimulated phosphoinositide turnover (PI turnover) only in those T-lymphocytes which had been preactivated by PHA with IL-2 and expressed the IL-2 receptors. The effect of PHA on PI turnover was, in general, stronger than that of IL-2. These results indicate that IL-2 and PHA-activated proliferation of human T-lymphocytes is accompanied by stimulation of PI turnover. However, IL-2-induced proliferative response may not be a direct consequence of PI turnover stimulation in these cells.     

Regulation of malonyl-CoA concentration and turnover in the normal heart

The goal of this study was to test the relationship between malonyl-CoA concentration and its turnover measured in isolated rat hearts perfused with NaH(13)CO(3). This turnover is a direct measurement of the flux of acetyl-CoA carboxylation in the intact heart. It also reflects the rate of malonyl-CoA decarboxylation, i.e. the only known fate of malonyl-CoA in the heart. Conditions were selected to result in stable malonyl-CoA concentrations ranging from 1.5 to 5 nmol.g wet weight-(1). The malonyl-CoA concentration was directly correlated with the turnover of malonyl-CoA, ranging from 0.7 to 4.2 nmol.min(-) (1).g wet weight(-1) (slope = 0.98, r(2) = 0.94). The V(max) activities of acetyl-CoA carboxylase and of malonyl-CoA decarboxylase exceeded the rate of malonyl-CoA turnover by 2 orders of magnitude and did not correlate with either concentration or turnover of malonyl-CoA. However, conditions of perfusion that increased acetyl-CoA supply resulted in higher turnover and concentration, demonstrating that malonyl-CoA turnover is regulated by the supply of acetyl-CoA. The only condition where the activity of malonyl-CoA decarboxylase regulated malonyl-CoA kinetics was when the enzyme was pharmacologically inhibited, resulting in increased malonyl-CoA concentration and decreased turnover. Our data show that, in the absence of enzyme inhibitors, the rate of acetyl-CoA carboxylation is the main determinant of the malonyl-CoA concentration in the heart.     

Indirect Methods Produce Higher Estimates of Fine Root Production and Turnover Rates than Direct Methods

The production and turnover of fine roots play substantial roles in the biogeochemical cycles of terrestrial ecosystems. However, the disparity among the estimates of both production and turnover, particularly due to technical limitations, has been debated for several decades. Here, we conducted a meta-analysis to compare published estimates of fine root production and turnover rates derived from different methods at the same sites and at the same sampling time. On average, the estimates of fine root production and turnover rates were 87% and 124% higher, respectively, by indirect methods than by direct methods. The substantially higher fine root production and turnover estimated by indirect methods, on which most global carbon models are based, indicate the necessity of re-assessing the global carbon model predictions for atmospheric carbon sequestration in soils as a result of the production and turnover of fine roots.     

In vitro degradation of the flavonol quercetin and of quercetin glycosides in the porcine hindgut

The present study investigated the microbial degradation of the plant flavonol quercetin and its naturally occurring glycosides isoquercitrin and rutin in the porcine hindgut. The experiments were carried out with the semicontinuous colon-simulation technique. The fluid and particle phase of pig hindgut contents from freshly slaughtered animals were used for the in vitro incubations. Following a five-day equilibration period, quercetin, isoquercitrin or rutin were administered to fermentation vessels and their turnover rate was determined. None of the flavonols affected parameters of microbial fermentation like pH, redox potential or VFA production. The turnover rate for isoquercitrin was seven times higher than the turnover for the fermentation fluid. The turnover rates for quercetin and rutin were four and twofold higher than fluid turnover, respectively. After administration of isoquercitrin or rutin, their aglycone quercetin was detected as an intermediary metabolite. Under sterile conditions using autoclaved incubation fluids and hindgut contents, turnover rates for quercetin and rutin were still higher than the fluid turnover in the fermentation vessels. This indicates a certain chemical instability of the flavonols and/or adsorption to ingesta particles. Thus, flavonols are subjected to microbial metabolism in the porcine hindgut. The glycosidic structure strongly influences the rate of metabolism.