bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing effects of forest management on microbial community structure in a central European beech forest
Authors: Grayston Susan J , Rennenberg Heinz
Published: November 2006

This study aimed to characterize the effects of forest management on soil microbial community structure and function in a European beech (Fagus sylvatica L.) forest. We used community level physiological profiles, phospholipid fatty acid (PLFA) profiles, microbial biomass, culturing, and respiration approaches to quantify soil microbial community structure and activity at two sites in a naturally regenerated beech forest subjected to intermediate and heavy thinning and control (unthinned) in southern Germany. PLFA showed that the northeast-facing (NE) site contained significantly greater bacterial and fungal biomass than the southwest-facing (SW) site. Heavy thinning (tree basal area reduction from 27 to 10 m2·ha–1) significantly reduced microbial biomass in the NE site, measured using fumigation–extraction, but both bacterial and fungal biomass increased with thinning on the SW site. Soil microbial activity was significantly higher in the control plots of the NE compared with the SW site and was significantly reduced by heavy thinning, again only on the NE site. Our findings are consistent with our initial hypotheses that contrasting N uptake by beech on these two sites after thinning may relate to differences in the soil microbial biomass, population structure and function on the two sites.
Multinomial logit estimation of a matrix growth model for tropical dry forests of eastern Bolivia
Authors: Boltz Frederick , Carter Douglas R
Published: November 2006

Multinomial logistic (MNL) regression was employed to estimate the transition probabilities of a matrix growth model for dry forests of the eastern Bolivian lowlands. Probabilities of mortality, stability, and upgrowth of a size and species group were estimated as a function of tree and stand attributes influencing growth and mortality. Data for model estimation were drawn from logged and undisturbed permanent sample plots (PSPs) measured over 6 and 7 years in Chiquitania forests south of Concepción, Santa Cruz, Bolivia. The estimated transition probabilities of the MNL models are not significantly different from those derived from PSP data by the conventional approach of employing simple mean proportions of observed movements per guild and size class. MNL estimation is advantageous in that it generates a smoother distribution of transition probabilities across size classes, correcting for variance in the data and model estimation errors imposed by limited samples. Moreover, the MNL approach allows deterministic, stochastic, and dynamic prediction of forest evolution, while preserving the simple linear form of matrix models that facilitates their integration into economic optimization studies.
Soil and pine foliage nutrient responses 15 years after competing-vegetation control and their correlation with growth for 13 loblolly pine plantations in the southern United States
Authors: Miller James H , Allen H Lee , Zutter Bruce R , Zedaker Shepard M , Newbold Ray A
Published: November 2006

Influences of competition-control treatments on long-term soil and foliar nutrition were examined using a regional data set (the Competition Omission Monitoring Project) that documents loblolly pine (Pinus taeda L.) plantation development for 15 years after early intensive woody and (or) herbaceous control. Examined were trends for macro nutrients in soils sampled at years 0 and 15 and in pine foliage at years 2, 6, and 15 and their correlations with one another and with pine growth. Early control treatments resulted in distinct plantation successional patterns with contrasting herbaceous and woody components, all under pine-dominated canopies. There was an overall decrease in soil nutrient concentrations after 15 years of pine-plantation management, while C, N, and Ca decreased most after vegetation control. Early herbaceous treatments resulted in significantly less foliar N and K at year 15 as well. Foliar nutrient contents and fascicle mass at year 2 tended to be better correlated with year-15 pine volume than values at year 6 or year 15. Year-15 P concentrations had the strongest correlations between soil and foliar nutrient levels (r = 0.71–0.77). By year 15, intensive pine culture and vegetation control had placed demands on soil nutrient supplies to support enhanced growth that have not yet been replaced.
CANONICAL COVARIANT FORMALISM FOR DIRAC–NAMBU–GOTO BOSONIC p-BRANES AND THE GAUSS–BONNET TOPOLOGICAL TERM IN STRING THEORY
Authors: ESCALANTE ALBERTO
Published: November 2006

Using a covariant and gauge invariant geometric structure constructed on the Witten covariant phase space for Dirac–Nambu–Goto bosonic p-branes propagating in a curved background, we find the canonically conjugate variables, and the relevant commutation relations are considered. We also find the canonical variables for the Gauss–Bonnet topological term in string theory.
GEOMETRIC PHASES, GAUGE SYMMETRIES AND RAY REPRESENTATION
Authors: FUJIKAWA KAZUO
Published: November 2006

The conventional formulation of the nonadiabatic (Aharonov–Anandan) phase is based on the equivalence class {eiα(t)ψ(t,x)} which is not a symmetry of the Schrödinger equation. This equivalence class when understood as defining generalized rays in the Hilbert space is not generally consistent with the superposition principle in interference and polarization phenomena. The hidden local gauge symmetry, which arises from the arbitrariness of the choice of coordinates in the functional space, is then proposed as a basic gauge symmetry in the nonadiabatic phase. This reformulation reproduces all the successful aspects of the nonadiabatic phase in a manner manifestly consistent with the conventional notion of rays and the superposition principle. The hidden local symmetry is thus identified as the natural origin of the gauge symmetry in both of the adiabatic and nonadiabatic phases in the absence of gauge fields, and it allows a unified treatment of all the geometric phases. The nonadiabatic phase may well be regarded as a special case of the adiabatic phase in this reformulation, contrary to the customary understanding of the adiabatic phase as a special case of the nonadiabatic phase. Some explicit examples of geometric phases are discussed to illustrate this reformulation.
IRROTATIONAL MOMENTUM FLUCTUATIONS CONDITIONING THE QUANTUM NATURE OF PHYSICAL PROCESSES
Authors: TZENOV STEPHAN I.
Published: November 2006

Starting from a simple classical framework and employing some stochastic concepts, the basic ingredients of the quantum formalism are recovered. It has been shown that the traditional axiomatic structure of quantum mechanics can be rebuilt, so that the quantum mechanical framework resembles to a large extent that of the classical statistical mechanics and hydrodynamics. The main assumption used here is the existence of a random irrotational component in the classical momentum. Various basic elements of the quantum formalism (calculation of expectation values, the Heisenberg uncertainty principle, the correspondence principle) are recovered by applying traditional techniques, borrowed from classical statistical mechanics.
INVERTED NEUTRINO MASS HIERARCHIES FROM U(1) SYMMETRIES
Authors: LEONTARIS G. K. , PSALLIDAS A. , VLACHOS N. D.
Published: November 2006

Motivated by effective low energy models of string origin, we discuss the neutrino masses and mixing within the context of the Minimal Supersymmetric Standard Model supplemented by a U(1) anomalous family symmetry and additional Higgs singlet fields charged under this extra U(1). In particular, we interpret the solar and atmospheric neutrino data assuming that there are only three left-handed neutrinos which acquire Majorana masses via a lepton number violating dimension-five operator. We derive the general form of the charged lepton and neutrino mass matrices when two different pairs of singlet Higgs fields develop nonzero vacuum expectation values and show how the resulting neutrino textures are related to approximate lepton flavor symmetries. We perform a numerical analysis for one particular case and obtain solutions for masses and mixing angles, consistent with experimental data.
ITERATED LOCAL LEAST SQUARES MICROARRAY MISSING VALUE IMPUTATION
Authors: CAI ZHIPENG , HEYDARI MAYSAM , LIN GUOHUI
Published: November 2006

Microarray gene expression data often contains multiple missing values due to various reasons. However, most of gene expression data analysis algorithms require complete expression data. Therefore, accurate estimation of the missing values is critical to further data analysis. In this paper, an Iterated Local Least Squares Imputation (ILLSimpute) method is proposed for estimating missing values. Two unique features of ILLSimpute method are: ILLSimpute method does not fix a common number of coherent genes for target genes for estimation purpose, but defines coherent genes as those within a distance threshold to the target genes. Secondly, in ILLSimpute method, estimated values in one iteration are used for missing value estimation in the next iteration and the method terminates after certain iterations or the imputed values converge. Experimental results on six real microarray datasets showed that ILLSimpute method performed at least as well as, and most of the time much better than, five most recent imputation methods.
OPTIMALLY-CONNECTED HIDDEN MARKOV MODELS FOR PREDICTING MHC-BINDING PEPTIDES
Authors: ZHANG CHENHONG , BICKIS MIKELIS G. , WU FANG-XIANG , KUSALIK ANTHONY J.
Published: November 2006

Hidden Markov models (HMMs) are one of various methods that have been applied to prediction of major histo-compatibility complex (MHC) binding peptide. In terms of model topology, a fully-connected HMM (fcHMM) has the greatest potential to predict binders, at the cost of intensive computation. While a profile HMM (pHMM) performs dramatically fewer computations, it potentially merges overlapping patterns into one which results in some patterns being missed. In a profile HMM a state corresponds to a position on a peptide while in an fcHMM a state has no specific biological meaning. This work proposes optimally-connected HMMs (ocHMMs), which do not merge overlapping patterns and yet, by performing topological reductions, a model's connectivity is greatly reduced from an fcHMM. The parameters of ocHMMs are initialized using a novel amino acid grouping approach called "multiple property grouping." Each group represents a state in an ocHMM. The proposed ocHMMs are compared to a pHMM implementation using HMMER, based on performance tests on two MHC alleles HLA (Human Leukocyte Antigen)-A*0201 and HLA-B*3501. The results show that the heuristic approaches can be adjusted to make an ocHMM achieve higher predictive accuracy than HMMER. Hence, such obtained ocHMMs are worthy of trial for predicting MHC-binding peptides.
SOME COMMENTS ON INSTABILITY OF FALSE DISCOVERY RATE ESTIMATION
Authors: QIU XING , YAKOVLEV ANDREI
Published: November 2006

Some extended false discovery rate (FDR) controlling multiple testing procedures rely heavily on empirical estimates of the FDR constructed from gene expression data. Such estimates are also used as performance indicators when comparing different methods for microarray data analysis. The present communication shows that the variance of the proposed estimators may be intolerably high, the correlation structure of microarray data being the main cause of their instability.
STRUCTURAL MODELING AND ANALYSIS OF SIGNALING PATHWAYS BASED ON PETRI NETS
Authors: LI CHEN , SUZUKI SHUNICHI , GE QI-WEI , NAKATA MITSURU , MATSUNO HIROSHI , MIYANO SATORU
Published: November 2006

The purpose of this paper is to discuss how to model and analyze signaling pathways by using Petri net. Firstly, we propose a modeling method based on Petri net by paying attention to the molecular interactions and mechanisms. Then, we introduce a new notion "activation transduction component" in order to describe an enzymic activation process of reactions in signaling pathways and shows its correspondence to a so-called elementary T-invariant in the Petri net models. Further, we design an algorithm to effectively find basic enzymic activation processes by obtaining a series of elementary T-invariants in the Petri net models. Finally, we demonstrate how our method is practically used in modeling and analyzing signaling pathway mediated by thrombopoietin as an example.
SYMBOLIC-NUMERIC ESTIMATION OF PARAMETERS IN BIOCHEMICAL MODELS BY QUANTIFIER ELIMINATION
Authors: ANAI HIROKAZU , ORII SHIGEO , HORIMOTO KATSUHISA
Published: November 2006

The sequencing of complete genomes allows analyses of the interactions between various biological molecules on a genomic scale, which prompted us to simulate the global behaviors of biological phenomena on the molecular level. One of the basic mathematical problems in the simulation is the parameter optimization in the kinetic model for complex dynamics, and many estimation methods have been designed. We introduce a new approach to estimate the parameters in biological kinetic models by quantifier elimination (QE), in combination with numerical simulation methods. The estimation method was applied to a model for the inhibition kinetics of HIV proteinase with ten parameters and nine variables, and attained the goodness of fit to 300 points of observed data with the same magnitude as that obtained by the previous estimation methods, remarkably by using only one or two points of data. Furthermore, the utilization of QE demonstrated the feasibility of the present method for elucidating the behavior of the parameters and the variables in the analyzed model. Therefore, the present symbolic-numeric method is a powerful approach to reveal the fundamental mechanisms of kinetic models, in addition to being a computational engine.
PATH-BASED SYSTEMS TO GUIDE SCIENTISTS IN THE MAZE OF BIOLOGICAL DATA SOURCES
Authors: COHEN-BOULAKIA SARAH , DAVIDSON SUSAN , FROIDEVAUX CHRISTINE , LACROIX ZOÉ , VIDAL MARIA-ESTHER
Published: November 2006

Fueled by novel technologies capable of producing massive amounts of data for a single experiment, scientists are faced with an explosion of information which must be rapidly analyzed and combined with other data to form hypotheses and create knowledge. Today, numerous biological questions can be answered without entering a wet lab. Scientific protocols designed to answer these questions can be run entirely on a computer.

Biological resources are often complementary, focused on different objects and reflecting various experts' points of view. Exploiting the richness and diversity of these resources is crucial for scientists. However, with the increase of resources, scientists have to face the problem of selecting sources and tools when interpreting their data.

In this paper, we analyze the way in which biologists express and implement scientific protocols, and we identify the requirements for a system which can guide scientists in constructing protocols to answer new biological questions. We present two such systems, BioNavigation and BioGuide dedicated to help scientists select resources by following suitable paths within the growing network of interconnected biological resources.
Cell cycle-dependent calcium oscillations in mouse embryonic stem cells
Authors: Kapur Nidhi , Mignery Gregory A. , Banach Kathrin
Published: November 2006

During cell cycle progression, somatic cells exhibit different patterns of intracellular Ca2+ signals during the G0 phase, the transition from G1 to S, and from G2 to M. Because pluripotent embryonic stem (ES) cells progress through cell cycle without the gap phases G1 and G2, we aimed to determine whether mouse ES (mES) cells still exhibit characteristic changes of intracellular Ca2+ concentration during cell cycle progression. With confocal imaging of the Ca2+-sensitive dye fluo-4 AM, we identified that undifferentiated mES cells exhibit spontaneous Ca2+ oscillations. In control cultures where 50.4% of the cells reside in the S phase of the cell cycle, oscillations appeared in 36% of the cells within a colony. Oscillations were not initiated by Ca2+ influx but depended on inositol 1,4,5-trisphosphate (IP3)-mediated Ca2+ release and the refilling of intracellular stores by a store-operated Ca2+ influx (SOC) mechanism. Using cell cycle synchronization, we determined that Ca2+ oscillations were confined to the G1/S phase (∼70% oscillating cells vs. G2/M with ∼15% oscillating cells) of the cell cycle. ATP induced Ca2+ oscillations, and activation of SOC could be induced in G1/S and G2/M synchronized cells. Intracellular Ca2+ stores were not depleted, and all three IP3 receptor isoforms were present throughout the cell cycle. Cell cycle analysis after EGTA, BAPTA-AM, 2-aminoethoxydiphenyl borate, thapsigargin, or U-73122 treatment emphasized that IP3-mediated Ca2+ release is necessary for cell cycle progression through G1/S. Because the IP3 receptor sensitizer thimerosal induced Ca2+ oscillations only in G1/S, we propose that changes in IP3 receptor sensitivity or basal levels of IP3 could be the basis for the G1/S-confined Ca2+ oscillations.
Mitochondria and neuronal activity
Authors: Kann Oliver , Kovács Richard
Published: November 2006

Mitochondria are central for various cellular processes that include ATP production, intracellular Ca2+ signaling, and generation of reactive oxygen species. Neurons critically depend on mitochondrial function to establish membrane excitability and to execute the complex processes of neurotransmission and plasticity. While much information about mitochondrial properties is available from studies on isolated mitochondria and dissociated cell cultures, less is known about mitochondrial function in intact neurons in brain tissue. However, a detailed description of the interactions between mitochondrial function, energy metabolism, and neuronal activity is crucial for the understanding of the complex physiological behavior of neurons, as well as the pathophysiology of various neurological diseases. The combination of new fluorescence imaging techniques, electrophysiology, and brain slice preparations provides a powerful tool to study mitochondrial function during neuronal activity, with high spatiotemporal resolution. This review summarizes recent findings on mitochondrial Ca2+ transport, mitochondrial membrane potential (ΔΨm), and energy metabolism during neuronal activity. We will first discuss interactions of these parameters for experimental stimulation conditions that can be related to the physiological range. We will then describe how mitochondrial and metabolic dysfunction develops during pathological neuronal activity, focusing on temporal lobe epilepsy and its experimental models. The aim is to illustrate that 1) the structure of the mitochondrial compartment is highly dynamic in neurons, 2) there is a fine-tuned coupling between neuronal activity and mitochondrial function, and 3) mitochondria are of central importance for the complex behavior of neurons.
Streptozotocin induces G2 arrest in skeletal muscle myoblasts and impairs muscle growth in vivo
Authors: Johnston Adam P. W. , Campbell Jonathan E. , Found Jeremy G. , Riddell Michael C. , Hawke Thomas J.
Published: November 2006

Streptozotocin (STZ) is used extensively to induce pancreatic β-cell death and ultimately diabetes mellitus in animal models. However, the direct effects of STZ on muscle are largely unknown. To delineate the effects of STZ from the effects of hypoinsulinemia/hyperglycemia, we injected young rats with 1) saline (control), 2) STZ (120 mg/kg) or 3) STZ and insulin (STZ-INS; to maintain euglycemia). STZ rats demonstrated significantly elevated blood glucose throughout the 48-h protocol, while control and STZ-INS rats were euglycemic. Body mass increased in control (13 ± 4 g), decreased by 19 ± 2 g in STZ and remained unchanged in STZ-INS rats (−0.3 ± 2 g). Cross-sectional areas of gastrocnemius muscle fibers were smaller in STZ vs. control (1,480 ± 149 vs. 1,870 ± 40 μm2, respectively; P < 0.05) and insulin treatment did not rescue this defect (STZ-INS: 1,476 ± 143 μm2). Western blot analysis revealed a detectable increase in ubiquitinated proteins in the STZ skeletal muscles compared with control and STZ-INS. To further define the effects of STZ on skeletal muscle, independent of hyperglycemia, myoblasts were exposed to varying doses of STZ (0.25–3.0mg/ml) in vitro. Both acute and chronic exposures of STZ significantly impaired proliferative capacity in a dose-dependent manner. Within STZ-treated myoblasts, increased reactive oxygen species was associated with significant G2/M phase cell-cycle arrest. Taken together, our findings show that the effects of STZ are not β-cell specific and reveal that STZ should not be used for studies examining diabetic myopathy.
Functional characterization of two S-nitroso-l-cysteine transporters, which mediate movement of NO equivalents into vascular cells
Authors: Li Sheng , Whorton A. Richard
Published: November 2006

System L amino acid transporters have been shown to be responsible for cellular uptake of S-nitroso-l-cysteine (l-CSNO). In this study, we examined the characteristics of l-CSNO uptake in Xenopus laevis oocytes expressing system L transporters and found that uptake increased only when both 4F2 heavy chain (4F2HC) and either L-type amino acid transporter 1 (LAT1) or LAT2 light chain were coexpressed. The Km for transport was 57 ± 8 μM for 4F2HC-LAT1 and 520 ± 52 μM for 4F2HC-LAT2. Vascular endothelial and smooth muscle cells were shown to express transcripts for 4F2HC and for both LAT1 and LAT2. Transport of l-CSNO into red blood cells, endothelial cells, and smooth muscle cells was inhibited by 2-aminobicyclo(2.2.1)heptane-2-carboxylic acid (BCH) and by large neutral amino acids demonstrating functional system L transporters in each cell type. Uptake of l-CSNO led to accumulation of cellular S-nitrosothiols and inhibition of both growth factor-induced ERK phosphorylation and TNF-α-mediated IκB degradation. Similar effects were seen when cells were incubated simultaneously with S-nitrosoalbumin and l-cysteine but not with d-cysteine or with S-nitrosoalbumin alone. In each case, nitrosylation of proteins and cellular responses were blocked by BCH. Together, these data suggest that transmembrane movement of nitric oxide (NO) equivalents from the plasma albumin NO reservoir is mediated by cysteine, which serves as a carrier. The mechanism requires transnitrosylation from S-nitrosoalbumin to free cysteine and activity of system L transporters, thereby providing a unique pathway for cellular responses to S-nitrosoalbumin.
N-WASP inhibitor wiskostatin nonselectively perturbs membrane transport by decreasing cellular ATP levels
Authors: Guerriero Christopher J. , Weisz Ora A.
Published: November 2006

Wiskott-Aldrich syndrome protein (WASP) and WAVE stimulate actin-related protein (Arp)2/3-mediated actin polymerization, leading to diverse downstream effects, including the formation and remodeling of cell surface protrusions, modulation of cell migration, and intracytoplasmic propulsion of organelles and pathogens. Selective inhibitors of individual Arp2/3 activators would enable more exact dissection of WASP- and WAVE-dependent cellular pathways and are potential therapeutic targets for viral pathogenesis. Wiskostatin is a recently described chemical inhibitor that selectively inhibits neuronal WASP (N-WASP)-mediated actin polymerization in vitro. A growing number of recent studies have utilized this drug in vivo to uncover novel cellular functions for N-WASP; however, the selectivity of wiskostatin in intact cells has not been carefully explored. In our studies with this drug, we observed rapid and dose-dependent inhibition of N-WASP-dependent membrane trafficking steps. Additionally, however, we found that addition of wiskostatin inhibited numerous other cellular functions that are not believed to be N-WASP dependent. Further studies revealed that wiskostatin treatment caused a rapid, profound, and irreversible decrease in cellular ATP levels, consistent with its global effects on cell function. Our data caution against the use of this drug as a selective perturbant of N-WASP-dependent actin dynamics in vivo.
Induction of early response genes in trypsin inhibitor-induced pancreatic growth
Authors: Guo Lili , Sans Maria Dolors , Gurda Grzegorz T. , Lee Sae-Hong , Ernst Stephen A. , Williams John A.
Published: November 2006

Endogenous CCK release induced by a synthetic trypsin inhibitor, camostat, stimulates pancreatic growth; however, the mechanisms mediating this growth are not well established. Early response genes often couple short-term signals with long-term responses. To study their participation in the pancreatic growth response, mice were fasted for 18 h and refed chow containing 0.1% camostat for 1–24 h. Expression of 18 early response genes were evaluated by quantitative PCR; mRNA for 17 of the 18 increased at 1, 2, 4, or 8 h. Protein expression for c-jun, c-fos, ATF-3, Egr-1, and JunB peaked at 2 h. Nuclear localization was confirmed by immunohistochemistry of c-fos, c-jun, and Egr-1. Refeeding regular chow induced only a small increase of c-jun and none in c-fos expression. JNKs and ERKs were activated 1 h after camostat feeding as was the phosphorylation of c-jun and ATF-2. AP-1 DNA binding evaluated by EMSA showed a significant increase 1–2 h after camostat feeding with participation of c-jun, c-fos, ATF-2, ATF-3, and JunB shown by supershift. The CCK antagonist IQM-95,333 blocked camostat feeding-induced c-jun and c-fos expression by 67 and 84%, respectively, and AP-1 DNA binding was also inhibited. In CCK-deficient mice, the maximal response of c-jun induction and AP-1 DNA binding were reduced by 64 and 70%, respectively. These results indicate that camostat feeding induces a spectrum of early response gene expression and AP-1 DNA binding and that these effects are mainly CCK dependent.
Postnatal ontogenesis of the circadian clock within the rat liver
Authors: Sládek Martin , Jindráková Zuzana , Bendová Zdenka , Sumová Alena
Published: November 2006

In mammals, the circadian oscillator within the suprachiasmatic nuclei (SCN) entrains circadian clocks in numerous peripheral tissues. Central and peripheral clocks share a molecular core clock mechanism governing daily time measurement. In the rat SCN, the molecular clockwork develops gradually during postnatal ontogenesis. The aim of the present work was to elucidate when during ontogenesis the expression of clock genes in the rat liver starts to be rhythmic. Daily profiles of mRNA expression of clock genes Per1, Per2, Cry1, Clock, Rev-Erbα, and Bmal1 were analyzed in the liver of fetuses at embryonic day 20 (E20) or pups at postnatal age 2 (P2), P10, P20, P30, and in adults by real-time RT-PCR. At E20, only a high-amplitude rhythm in Rev-Erbα and a low-amplitude variation in Cry1 but no clear circadian rhythms in expression of other clock genes were detectable. At P2, a high-amplitude rhythm in Rev-Erbα and a low-amplitude variation in Bmal1 but no rhythms in expression of other genes were detected. At P10, significant rhythms only in Per1 and Rev-Erbα expression were present. At P20, clear circadian rhythms in the expression of Per1, Per2, Rev-Erbα, and Bmal1, but not yet of Cry1 and Clock, were detected. At P30, all clock genes were expressed rhythmically. The phase of the rhythms shifted between all studied developmental periods until the adult stage was achieved. The data indicate that the development of the molecular clockwork in the rat liver proceeds gradually and is roughly completed by 30 days after birth.
Influence of endurance exercise training and sex on intramyocellular lipid and mitochondrial ultrastructure, substrate use, and mitochondrial enzyme activity
Authors: Tarnopolsky Mark A. , Rennie Courtney D. , Robertshaw Holly A. , Fedak-Tarnopolsky Stephanie N. , Devries Michaela C. , Hamadeh Mazen J.
Published: November 2006

Impaired mitochondrial function and structure and intramyocellular lipid (IMCL) accumulation have been associated with obesity and Type 2 diabetes. We examined whether endurance exercise training and sex influenced IMCL and mitochondrial morphology using electron microscopy, whole-body substrate use, and mitochondrial enzyme activity. Untrained men ( n = 5) and women ( n = 7) were tested before and after 7 wk of endurance exercise training. Testing included 90 min of cycle ergometry at 60% V̇o2 peak with preexercise muscle biopsies analyzed for IMCL and mitochondrial size/area using electron microscopy and short-chain β-hydroxyacyl-CoA dehydrogenase (SCHAD) and citrate synthase (CS) enzyme activity. Training increased the mean lipid area density ( P = 0.090), the number of IMCL droplets ( P = 0.055), the number of IMCL droplets in contact with mitochondria ( P = 0.010), the total mitochondrial area ( P < 0.001), and the size of individual mitochondrial fragments ( P = 0.006). Women had higher mean lipid area density ( P = 0.030) and number of IMCL droplets ( P = 0.002) before and after training, but higher individual IMCL area only before training ( P = 0.013), compared with men. Women oxidized more fat ( P = 0.027) and less carbohydrate ( P = 0.032) throughout the study. Training increased V̇o2 peak ( P < 0.001), %fat oxidation ( P = 0.018), SCHAD activity ( P = 0.003), and CS activity ( P = 0.042). In summary, endurance exercise training increased IMCL area density due to an increase in the number of lipid droplets, whereas the increase in total mitochondrial area was due to an increase in the size of individual mitochondrial fragments. In addition, women have higher IMCL content compared with men due mainly to a greater number of individual droplets. Finally, endurance exercise training increased the proportion of IMCL in physical contact with mitochondria.
Effects of the menstrual cycle and sex on postexercise hemodynamics
Authors: Lynn Brenna M. , McCord Jennifer L. , Halliwill John R.
Published: November 2006

Factors associated with the menstrual cycle, such as the endogenous hormones estrogen and progesterone, have dramatic effects on cardiovascular regulation. It is unknown how this affects postexercise hemodynamics. Therefore, we examined the effects of the menstrual cycle and sex on postexercise hemodynamics. We studied 14 normally menstruating women [24.0 (4.2) yr; SD] and 14 men [22.5 (3.5) yr] before and through 90 min after cycling at 60% V̇o2 peak for 60 min. Women were studied during their early follicular, ovulatory, and mid-luteal phases; men were studied once. In men and women during all phases studied, mean arterial pressure was decreased after exercise throughout 60 min ( P < 0.001) postexercise and returned to preexercise values at 90 min ( P = 0.089) postexercise. Systemic vascular conductance was increased following exercise in both sexes throughout 60 min ( P = 0.005) postexercise and tended to be elevated at 90 min postexercise ( P = 0.052), and femoral vascular conductance was increased following exercise throughout 90 min ( P < 0.001) postexercise. Menstrual phase and sex had no effect on the percent reduction in arterial pressure ( P = 0.360), the percent rise in systemic vascular conductance ( P = 0.573), and the percent rise in femoral vascular conductance ( P = 0.828) from before to after exercise, nor did the pattern of these responses differ across recovery with phase or sex. This suggests that postexercise hemodynamics are largely unaffected by sex or factors associated with the menstrual cycle.
Prenatal programming of rat proximal tubule Na+/H+ exchanger by dexamethasone
Authors: Dagan Amit , Gattineni Jyothsna , Cook Vodi , Baum Michel
Published: November 2006

Prenatal administration of dexamethasone causes hypertension in rats when they are studied as adults. Although an increase in tubular sodium reabsorption has been postulated to be a factor programming hypertension, this has never been directly demonstrated. The purpose of this study was to examine whether prenatal programming by dexamethasone affected postnatal proximal tubular transport. Pregnant Sprague-Dawley rats were injected with intraperitoneal dexamethasone (0.2 mg/kg) daily for 4 days between the 15th and 18th days of gestation. Prenatal dexamethasone resulted in an elevation in systolic blood pressure when the rats were studied at 7–8 wk of age compared with vehicle-treated controls: 131 ± 3 vs. 115 ± 3 mmHg ( P < 0.001). The rate of proximal convoluted tubule volume absorption, measured using in vitro microperfusion, was 0.61 + 0.07 nl·mm−1·min−1 in control rats and 0.93+ 0.07 nl·mm−1·min−1 in rats that received prenatal dexamethasone ( P < 0.05). Na+/H+ exchanger activity measured in perfused tubules in vitro using the pH-sensitive dye BCECF showed a similar 50% increase in activity in proximal convoluted tubules from rats treated with prenatal dexamethasone. Although there was no change in abundance of NHE3 mRNA, the predominant luminal proximal tubule Na+/H+ exchanger, there was an increase in NHE3 protein abundance on brush-border membrane vesicles in 7- to 8-wk-old rats receiving prenatal dexamethasone. In conclusion, prenatal administration of dexamethasone in rats increases proximal tubule transport when rats are studied at 7–8 wk old, in part by stimulating Na+/H+ exchanger activity. The increase in proximal tubule transport may be a factor mediating the hypertension by prenatal programming with dexamethasone.
The spatial-temporal redistribution of pulmonary blood flow with postnatal growth
Authors: Glenny Robb W. , Bernard Susan L. , Luchtel Daniel L. , Neradilek Blazej , Polissar Nayak L.
Published: November 2006

The pulmonary vascular tree undergoes remarkable postnatal development and remodeling. While a number of studies have characterized longitudinal changes in vascular function with growth, none have explored regional patterns of vascular remodeling. We therefore studied six neonatal pigs to see how regional blood flow changes with growth. We selected pigs because of their rapid growth and their similarities to human development with respect to the pulmonary vascular tree. Fluorescent microspheres of varying colors were injected into the pulmonary circulation to mark regional blood on days 3, 12, 27, 43, and 71 after birth. The animals were awake and in the prone posture for all injections. The lungs were subsequently removed, air dried, and sectioned into ∼2-cm3 pieces. Flow on each injection day was determined for each piece. Despite the increase in the hydrostatic gradient in the lung with growth, there was a strong correlation between blood flow to the same lung piece when compared on days 3 and 71 (0.73 ± 0.12). Although a dorsal-ventral gradient of perfusion did not exist on day 3, blood flow increased more in the dorsal region by day 12 and then gradually became more uniform by day 71. Although most of the lung pieces did not show any discernable pattern of blood flow redistribution, there were spatial patterns of blood flow redistribution that were similar across animals. Our findings suggest that local mechanisms, shared across animals, guide regional changes in vascular resistance or vasoregulation during postnatal development. In the pig, these mechanisms act to produce more uniform flow in the normal posture for an ambulating quadruped. The stimuli for these changes have not yet been identified.
Rat Nucleus Accumbens Neurons Persistently Encode Locations Associated With Morphine Reward
Authors: German Paul W. , Fields Howard L.
Published: November 2006

When rats and mice are free to explore a familiar environment they spend more time in a previously rewarded location. This conditioned place preference (CPP) results from an increased probability of initiating transitions from an unrewarded location to one previously paired with reward. We recorded nucleus accumbens (NAc) neurons while rats explored a three-room in-line apparatus. Before place conditioning, approximately equal proportions of NAc neurons show excitations or inhibitions when the rat is in each of the rooms (morphine paired, center or saline paired). Conditioning increased the proportion of neurons inhibited while the rat was in the morphine room and neurons excited in the saline room. Many of the neurons in these two groups responded during room transitions. Furthermore, the postconditioning increase in the population of neurons with room-selective responding persisted for several weeks after the last morphine treatment. This long-lasting change in population responses of NAc neurons to initially neutral locations is a neural correlate of the change in location preference manifest as CPP.
Adenosine Inhibits Activity of Hypocretin/Orexin Neurons by the A1 Receptor in the Lateral Hypothalamus: A Possible Sleep-Promoting Effect
Authors: Liu Zhong-Wu , Gao Xiao-Bing
Published: November 2006

Neurons in the lateral hypothalamus (LH) that contain hypocretin/orexin have been established as important promoters of arousal. Deficiencies in the hypocretin/orexin system lead to narcolepsy. The inhibition of hypocretin/orexin neurons by sleep-promoting neurotransmitters has been suggested as one part of the sleep regulation machinery. Adenosine has been identified as a sleep promoter and its role in sleep regulation in the basal forebrain has been well documented. However, the effect of adenosine on arousal-promoting hypocretin/orexin neurons has not been addressed, despite recent evidence that immunocytochemical visualization of adenosine receptors was detected in these neurons. In this study, we examined the hypothesis that adenosine inhibits the activity of hypocretin/orexin neurons by using electrophysiological methods in brain slices from mice expressing green fluorescent protein in hypocretin/orexin neurons. We found that adenosine significantly attenuated the frequency of action potentials without a change in membrane potential in hypocretin/orexin neurons. The adenosine-mediated inhibition arises from depression of excitatory synaptic transmission to hypocretin/orexin neurons because adenosine depresses the amplitude of evoked excitatory postsynaptic potential and the frequency of spontaneous and miniature excitatory postsynaptic currents in these neurons. At the cell body of the hypocretin/orexin neurons, adenosine inhibits voltage-dependent calcium currents without the induction of GIRK current. The inhibitory effect of adenosine is dose dependent, pertussis toxin sensitive, and mediated by A1 receptors. In summary, our data suggest that in addition to its effect in the basal forebrain, adenosine exerts its sleep-promoting effect in the LH by inhibition of hypocretin/orexin neurons.
Metabotropic Glutamate Receptors in the Main Olfactory Bulb Drive Granule Cell-Mediated Inhibition
Authors: Heinbockel Thomas , Laaris Nora , Ennis Matthew
Published: November 2006

Main olfactory bulb (MOB) granule cells (GCs) express high levels of the group I metabotropic glutamate receptor (mGluR), mGluR5. We investigated the role of mGluRs in regulating GC activity in rodent MOB slices using whole cell patch-clamp electrophysiology. The group I/II mGluR agonist (±)-1-aminocyclopentane- trans-1,3-dicarboxylic acid (ACPD) or the selective group I agonist (RS)-3,5-dihydroxyphenylglycine (DHPG) depolarized (∼20 mV) and increased the firing rate of GCs. In the presence of ionotropic glutamate and GABA receptor antagonists, DHPG evoked a more modest depolarization (∼8 mV). In voltage clamp, DHPG, but not group II [(2S,2′R,3)-2-(2′,3′-dicarboxycyclopropyl)glycine, DCG-IV] or group III [L(+)-2-amino-4-phosphonobutyric acid, L-AP4] mGluR agonists, induced an inward current. The inward current reversed polarity near the potassium equilibrium potential, suggesting mediation by closure of potassium channels. The DHPG-evoked inward current was unaffected by the mGluR1 antagonist ( S)-(+)-α-amino-4-carboxy-2-methylbenzeneacetic acid (LY367385), was blocked by the group I/II mGluR antagonist (α S)-α-amino-α-[(1 S,2 S)-2-carboxycyclopropyl]-9H-xanthine-9-propanoic acid (LY341495), and was absent in GCs from mGluR5 knockout mice. LY341495 also attenuated mitral cell-evoked voltage-sensitive dye signals in the external plexiform layer and mitral cell-evoked spikes in GCs. These results suggest that activation of mGluR5 increases GC excitability, an effect that should increase GC-mediated GABAergic inhibition of mitral cells. In support of this: DHPG increased the frequency of spontaneous GABAergic inhibitory postsynaptic currents in mitral cells and LY341495 attenuated the feedback GABAergic postsynaptic potential elicited by intracellular depolarization of mitral cells. Our results suggest that activation of mGluR5 participates in feedforward and/or feedback inhibition at mitral cell to GC dendrodendritic synapses, possibly to modulate lateral inhibition and contrast in the MOB.
Differential Effects of Hypothermia on Early and Late Epileptiform Events After Severe Hypoxia in Preterm Fetal Sheep
Authors: Bennet L. , Dean J. M. , Wassink G. , Gunn A. J.
Published: November 2006

Moderate cerebral hypothermia is consistently neuroprotective after experimental hypoxia-ischemia; however, its mechanisms remain poorly defined. Using a model of complete umbilical cord occlusion for 25 min in 0.7 gestation fetal sheep, we examined the effects of cerebral hypothermia (fetal extradural temperature reduced from 39.5 ± 0.2°C to <34°C; mean ± SD), from 90 min to 70 h after the end of the insult, on postocclusion epileptiform activity. In the first 6 h after the end of occlusion, fetal electroencephalographic (EEG) activity was abnormal with a mixture of fast and slow epileptiform transients superimposed on a suppressed background; seizures started a mean of 8 h after occlusion. There was a close correlation between numbers of these EEG transients and subsequent neuronal loss in the striatum after 3 days recovery ( r2= 0.65, P = 0.008). Hypothermia was associated with a marked reduction in numbers of epileptiform transients in the first 6 h, reduced amplitude of seizures, and reduced striatal neuronal loss. In conclusion, neuroprotection with delayed, prolonged head cooling after a severe asphyxial insult in the preterm fetus was associated with potent, specific suppression of epileptiform transients in the early recovery phase but not of numbers of delayed seizures.
Morphological and Electrophysiological Properties of GABAergic and Non-GABAergic Cells in the Deep Cerebellar Nuclei
Authors: Uusisaari Marylka , Obata Kunihiko , Knöpfel Thomas
Published: November 2006

The deep cerebellar nuclei (DCN) integrate inputs from the brain stem, the inferior olive, and the spinal cord with Purkinje cell output from cerebellar cortex and provide the major output of the cerebellum. Despite their crucial function in motor control and learning, the various populations of neurons in the DCN are poorly defined and characterized. Importantly, differences in electrophysiological properties between glutamatergic and GABAergic cells of the DCN have been largely elusive. Here, we used glutamate decarboxylase (GAD) 67-green fluorescent protein (GFP) knock-in mice to unambiguously identify GABAergic (GAD-positive) and non-GABAergic (GAD-negative, most likely glutamatergic) neurons of the DCN. Morphological analysis of DCN neurons patch-clamped with biocytin-containing electrodes revealed a significant overlap in the distributions of the soma sizes of GAD-positive and GAD-negative cells. Compared with GAD-negative DCN neurons, GAD-positive DCN neurons fire broader action potentials, display stronger frequency accommodation, and do not reach as high firing frequencies during depolarizing current injections. Furthermore, GAD-positive cells display slower spontaneous firing rates and have a more shallow frequency-to-current relationship than the GAD-negative cells but exhibit a longer-lasting rebound depolarization and associated spiking after a transient hyperpolarization. In contrast to the rather homogeneous population of GAD-positive cells, the GAD-negative cells were found to consist of two distinct populations as defined by cell size and electrophysiological features. We conclude that GABAergic DCN neurons are specialized to convey phasic spike rate information, whereas tonic spike rate is more faithfully relayed by the large non-GABAergic cells.
Motor-Unit Synchrony Within and Across Compartments of the Human Flexor Digitorum Superficialis
Authors: McIsaac Tara L. , Fuglevand Andrew J.
Published: November 2006

An interesting feature of the muscular organization of the human hand is that the main flexors and extensors of the fingers are compartmentalized and give rise to multiple parallel tendons that insert onto all the fingers. Previous studies of motor-unit synchrony in extensor digitorum and flexor digitorum profundus indicated that synaptic input to motor neurons supplying these multitendoned muscles is not uniformly distributed across the entire pool of motor neurons but instead appears to be partially segregated to supply subsets of motor neurons that innervate different muscular compartments. Little is known, however, about the organization of the synaptic inputs to the motor neurons supplying another multitendoned finger muscle, the flexor digitorum superficialis (FDS). Therefore in this study, we estimated the extent of divergence of last-order inputs to FDS motor neurons by measuring the degree of short-term synchrony among motor units within and across compartments of FDS. The degree of synchrony for motor-unit pairs within the same digit compartment was nearly twofold that of pairs of motor units in adjacent compartments and more than fourfold that of pairs in nonadjacent compartments. Therefore like other multitendoned muscles of the hand, last-order synaptic inputs to motor neurons supplying the FDS appear to primarily supply subsets of motor neurons innervating specific finger compartments. Such an organization presumably enables differential activation of separate compartments to facilitate independent movements of the fingers.
ATP-Binding Cassette Cholesterol Transporters and Cardiovascular Disease
Authors: Oram John F. , Vaughan Ashley M.
Published: November 2006

A hallmark of atherosclerotic cardiovascular disease (CVD) is the accumulation of cholesterol in arterial macrophages. Factors that modulate circulating and tissue cholesterol levels have major impacts on initiation, progression, and regression of CVD. Four members of the ATP-binding cassette (ABC) transporter family play important roles in this modulation. ABCA1 and ABCG1 export excess cellular cholesterol into the HDL pathway and reduce cholesterol accumulation in macrophages. ABCG5 and ABCG8 form heterodimers that limit absorption of dietary sterols in the intestine and promote cholesterol elimination from the body through hepatobiliary secretion. All 4 transporters are induced by the same sterol-sensing nuclear receptor system. ABCA1 expression and activity are also highly regulated posttranscriptionally by diverse processes.
ABCA1
mutations can cause a severe HDL-deficiency syndrome characterized by cholesterol deposition in tissue macrophages and prevalent atherosclerosis.
ABCG5
or
ABCG8
mutations can cause sitosterolemia, in which patients accumulate cholesterol and plant sterols in the circulation and develop premature CVD. Disrupting
Abca1
or
Abcg1
in mice promotes accumulation of excess cholesterol in macrophages, and manipulating mouse macrophage ABCA1 expression affects atherogenesis. Overexpressing ABCG5 and ABCG8 in mice attenuates diet-induced atherosclerosis in association with reduced circulating and liver cholesterol. Metabolites elevated in individuals with the metabolic syndrome and diabetes destabilize ABCA1 protein and inhibit transcription of all 4 transporters. Thus, impaired ABC cholesterol transporters might contribute to the enhanced atherogenesis associated with common inflammatory and metabolic disorders. Their beneficial effects on cholesterol homeostasis have made these transporters important new therapeutic targets for preventing and reversing CVD.