Mapping quantitative trait loci for binary trait in the F2:3 design

In the analysis of inheritance of quantitative traits with low heritability, an F_2:3 design that genotypes plants in F₂ and phenotypes plants in F_2:3 progeny is often used in plant genetics. Although statistical approaches for mapping quantitative trait loci (QTL) in the F_2:3 design have been well developed, those for binary traits of biological interest and economic importance are seldom addressed. In this study, an attempt was made to map binary trait loci (BTL) in the F_2:3 design. The fundamental idea was: the F₂ plants were genotyped, all phenotypic values of each F_2:3 progeny were measured for binary trait, and these binary trait values and the marker genotype informations were used to detect BTL under the penetrance and liability models. The proposed method was verified by a series of Monte-Carlo simulation experiments. These results showed that maximum likelihood approaches under the penetrance and liability models provide accurate estimates for the effects and the locations of BTL with high statistical power, even under of low heritability. Moreover, the penetrance model is as efficient as the liability model, and the F_2:3 design is more efficient than classical F₂ design, even though only a single progeny is collected from each F_2:3 family. With the maximum likelihood approaches under the penetrance and the liability models developed in this study, we can map binary traits as we can do for quantitative trait in the F_2:3 design.     

Evidence for H2O2 as the product of reduction of oxygen by alternative oxidase in mitochondria from potato tubers

Oxygen consumption by alternative oxidase (AOX), present in mitochondria of many angiosperms, is known to be cyanide-resistant in contrast to cytochrome oxidase. Its activity in potato tuber (Solanum tuberosum L.) was induced following chilling treatment at 4 °C. About half of the total O₂ consumption of succinate oxidation in such mitochondria was found to be sensitive to SHAM, a known inhibitor of AOX activity. Addition of catalase to the reaction mixture of AOX during the reaction decreased the rate of SHAM-sensitive oxygen consumption by nearly half, and addition at the end of the reaction released nearly half of the consumed oxygen by AOX, both typical of catalase action on H₂O₂. These findings with catalase suggest that the product of reduction of AOX is H₂O₂ and not H₂O, as previously surmised. In potatoes subjected to chill stress (4 °C) for periods of 3, 5 and ?8 days the activity of AOX in mitochondria increased progressively with a corresponding increase in the AOX protein detected by immunoblot of the protein.     

Selection of suitable reference genes for quantitative real-time PCR in trabecular meshwork cells under oxidative stress

Oxidative stress-induced dysfunction in trabecular meshwork (TM) cells is considered a major alteration that can lead to glaucoma. Hydrogen peroxide (H₂O₂) is the most widely used agent for inducing oxidation in TM cells in vitro. Quantitative real-time PCR (qPCR) is an important method for studying alterations in gene expression, and suitable (i.e. invariant) reference genes must be defined to normalize expression levels. In this study, eight common reference genes, i.e. PRS18, ACTB, B2M, GAPDH, PPIA, HPRT1, YWHAZ, and TBP, were evaluated for use in studies of H₂O₂-induced dysfunction in TM cells. Three established algorithms, geNorm, NormFinder, and BestKeeper, were used to analyze the reference genes. ACTB expression was least affected by H₂O₂ treatment in TM cells, and the combination of PPIA and HPRT1 was the most suitable gene pair for normalization. GAPDH and TBP were the most unstable genes and accordingly should be avoided in experiments with TM cells. These results provide a foundation for analyses of the mechanisms underlying glaucoma, and emphasize the importance of selecting suitable reference genes for qPCR studies.     

Quantitative aspects of oxygen and carbon dioxide exchange through the lungs in Ocypode ceratophthalmus (Crustacea: Decapoda) during rest and exercise in water and air

Ghost crabs Ocypode ceratophthalmus were exercised in air and water to measure CO₂ and O₂ exchange rates using the method of instantaneous measurements of oxygen consumption rate (MO₂) where applicable. Average heart rate increased from 100 to nearly 400 pulses per minute after five minutes of exercise on a treadmill at a run rate of 0.133 m s^?1. It took less than a minute for oxygen taken up through the lung epithelium from the air inside the branchial cavity to reach the maximal oxygen consumption rate of 26.1 mmol O₂ kg^?1 h^?1. Resting MO₂ was 4.06 mmol O₂ kg^?1 h^?1 in air, but decreased to 3.37 mmol O₂ kg^?1 h^?1 in seawater. Radioactive CO₂ from injected l-lactate is released linearly by the lung. The percent accumulated 14-CO₂ in exhaled air, plotted against time, intersects zero time on the x -axis, indicating rapid gas exchange at the lung surface. The P ₅₀ values for native haemocyanin of 4.89 mm Hg before exercise, and 8.99 mm Hg after exercise, are typical of a high-affinity haemocyanin usually associated with terrestrial crabs. The current notion that Ocypode ceratophthalmus drown when submerged in seawater was not substantiated by our experiments. MO₂ in seawater increased from 3.37 mmol O₂ kg^?1 h^?1 for resting crabs to 5.72 mmol O₂ kg^?1 h^?1 during exercise. When submerged by wave-seawater in the natural environment and during exercise in respirometer-seawater O. ceratophthalmus do not swim but, having a specific density of 1.044, float nearly weightless with a minimum of body movements.     

A numerical model for blood oxygenation in the pulmonary capillaries — Effect of pulmonary membrane resistance

A study of the blood oxygenation in pulmonary capillaries is made by considering the transport mechanisms of molecular diffusion, convection and the facilitated diffusion due to the presence of haemoglobin. The resistance offered by the pulmonary membrane on the transport of gases has been incorporated. The resulting system of coupled, non-linear partial differential equations is solved numerically.

It is found that, in the immediate neighbourhood of the entry, the amount of dissolved O₂ decreases. This decreases further as the resistance offered by the pulmonary membrane increases. The rate of oxygenation of blood increases as the permeability coefficient for O₂(P_o) increases. It is shown that the ideally permeable case for both O₂ and CO₂ can be approximated by taking P_o ˜ 10 cm/s. Further, it is shown that the oxygen takes longest and CO₂ is the fastest to attain equilibration. The equilibration length increases as the resistance offered by the membrane increases. Finally, some of the pulmonary diseases such as pulmonary oedema and fibrosis have been analyzed.     

A sensitive,simultaneous analysis of ribulose 1,5-bisphosphate carboxylase/oxygenase efficiencies: Graphical determination of the CO2/O2 specificity factor

A simple approach to determine CO₂/O₂ specificity factor () of ribulose 1,5-bisphosphate carboxylase/oxygenase is described. The assay measures the amount of CO₂ fixation at varying [CO₂]/[O₂] ratios after complete consumption of ribulose 1,5-bisphosphate (RuBP). Carbon dioxide fixation catalyzed by the carboxylase was monitored by directly measuring the moles of ¹⁴CO₂ incorporated into 3-phosphoglycerate (PGA). This measurement at different [CO₂]/[O₂] ratios is used to determine graphically by several different linear plots the total RuBP consumed by the two activities and the CO₂/O₂ specificity factor. The assay can be used to measure the amounts of products of the carboxylase and oxygenase reactions and to determine the concentration of the substrate RuBP converted to an endpoint amount of PGA and phosphoglycolate. The assay was found to be suitable for all [CO₂]/[O₂] ratios examined, ranging from 14 to 215 micromolar CO₂ (provided as 1–16 mM NaHCO₃) and 614 micromolar O₂ provided as 50% O₂. The procedure described is extremely rapid and sensitive. Specificity factors for enzymes of highly divergent values are in good agreement with previously published data.Abbreviations HEPPS N-(2-hydroxyethyl)piperazine-N-(3-propanesulfonic acid) - L large subunit of rubisco - PGA 3-phosphoglyceric acid - rubisco ribulose 1,5-bisphosphate carboxylase/oxygenase - RuBP d-ribulose 1,5-bisphosphate - S small subunit of rubisco - XuBP d-xylulose 1,5-bisphosphate     

Optimization of the bare platinum electrode as an oxygen measurement system in photosynthesis

This paper is concerned with the definition of the standard conditions required for optimum operation of the bare platinum electrode with photosynthetic samples. Experimental evidence shows the following: 1) Polarization circuits should have zero resistance; 2) The electrolyte layer between the electrodes should have a conductance higher than 54×10^{–6 –1} per mm² of platinum electrode area; 3) The electrodes should be polarized just before taking the measurements. All these facts can be interpreted in terms of phenomena occurring on the electrode: The adsorption of hydrogen on the electrode imposes the need for low resistances in the system, and oxygen consumption by the electrode is minimized by polarizing the electrodes as late as possible. This investigation increases the reliability of the bare platinum electrode and gives a basis for a comparison of the results from different experiments. Demonstrations of the pertinence of these conditions are made in our lab with the algae Dunaliella Tertiolecta.     

A clue to the origin of life: begin from making tools

The small molecules already existing on the earth can be assembled to biological macromolecules in the presence of the suitable tool. A workman must sharpen his tools if he is to do his work well. The tool must be specific, delicate and automatic. Obviously, it is enzyme. Therefore, to explore the origin of life we must understand the origin of the manufacturing tool of biological macromolecules—the origin of enzymes. We can understand more about the origin and evolution procedures of enzymes from the NO₂. NO₂ can easily form the dimmer, N₂O₄. Four N₂O₄ molecules can coordinate with a suitable metal ion and form a plane super molecule with four N₂O₄ molecules. This supramolecule provides the basis for the appearance of enzymes: (1) It is the template for producing enzymes. (2) It provides the active centers for enzymes. (3) It provides for the enzymes with specific function of chiral selection. This supramolecule reacts with formaldehyde and porphyrin compound is gradually formed. Once suitable function groups are substituted on the porphyrin ring, enzymes are formed. The primitive environment of earth can easily produce NO₂ and CH₂O. Therefore, this might be one clue to the origin of life.

Activation/deactivation of acetylcholinesterase by H2O2: more evidence for oxidative stress in vitiligo

Previously it has been demonstrated that the human epidermis synthesises and degrades acetylcholine and expresses both muscarinic and nicotinic receptors. These cholinergic systems have been implicated in the development of the epidermal calcium gradient and differentiation in normal healthy skin. In vitiligo severe oxidative stress occurs in the epidermis of these patients with accumulation of H2O2 in the 10(-3)M range together with a decrease in catalase expression/activity due to deactivation of the enzyme active site. It was also shown that the entire recycling of the essential cofactor (6R)-l-erythro-5,6,7,8-tetrahydrobiopterin via pterin-4a-carbinolamine dehydratase (PCD) and dihydropteridine reductase (DHPR) is affected by H2O2 oxidation of Trp/Met residues in the enzyme structure leading to deactivation of these proteins. Using fluorescence immunohistochemistry we now show that epidermal H2O2 in vitiligo patients yields also almost absent epidermal acetylcholinesterase (AchE). A kinetic analysis using pure recombinant human AchE revealed that low concentrations of H2O2 (10(-6)M) activate this enzyme by increasing the Vmax>2-fold, meanwhile high concentrations of H2O2 (10(-3)M) inhibit the enzyme with a significant decrease in Vmax. This result was confirmed by fluorescence excitation spectroscopy following the Trp fluorescence at lambdamax 280nm. Molecular modelling based on the established 3D structure of human AchE supported that H2O2-mediated oxidation of Trp(432), Trp(435), and Met(436) moves and disorients the active site His(440) of the enzyme, leading to deactivation of the protein. To our knowledge these results identified for the first time H2O2 regulation of AchE. Moreover, it was shown that H2O2-mediated oxidation of AchE contributes significantly to the well-established oxidative stress in vitiligo.     

Changes in haemorheology in the racing greyhound as related to oxygen delivery

Arterial blood samples were obtained from six greyhounds during rest, immediately before, and after a 704-m (7/16th mile) race. Measurements were made of various haematological (red cell count, haemoglobin, packed cell volume, white cell count, plasma proteins) and haemorheological variables. Blood and plasma viscosity were determined at high wall shear stresses (67-200 dynes.cm-2, 670-2000 microN.cm-2) in a 20-microns glass capillary device which was designed to take the diameter dependence of blood viscosity (Fahraeus-Lindqvist effect) into account. Compared to values at rest, substantial haemoconcentration occurred before the race, mainly due to splenic discharge of red cells. Additional haemoconcentration was found after the race. The increase of effective blood viscosity caused by elevation of packed cell volume was greater than the increase in O2 binding capacity resulting from the elevated haemoglobin concentration, suggesting that the haemoconcentration observed in the exercising greyhound does not enhance O2 delivery to skeletal muscle. The main physiological effect of red cell discharge from the contracting spleen appeared to be a consequence of the volume rather than the composition of the circulating blood.     

Microbial manganese(II) oxidation in the marine environment: a quantitative study

A great number of important chemical reactions that occur in the environment are microbially mediated. In order to understand the kinetics of these reactions it is necessary to develop methods to directly measure in situ reaction rates and to develop models to help elucidate the mechanisms of microbial catalysis. The oxidation of Mn(II) in a zone above the O₂/H₂S interface in Saanich Inlet, B.C., Canada is one such reaction. We present here a method by which in situ rates of microbial Mn(II) oxidation are measured and a model based on our experimental results to describe the general mechanism of Mn(H) oxidation. We propose a two step process in which Mn(II) is first bound by a site on the bacterial surface and then oxidized. The model is analogous to the Langmuir isotherm model for surface catalyzed gas reactions or the Michaelis-Menten model for enzyme kinetics. In situ Mn(II) oxidation rates were measured during five cruises to Saanich Inlet during the summers of 1983 and 1984. We use the model to calculate the apparent equilibrium binding constant (K_s 0.18 M), the apparent half saturation constant for biological Mn(H) oxidation (K_m = 0.22 to 0.89 M), the maximum rate of Mn(II) oxidation (V_max = 3.5 to 12.1 nM·h^-1) and the total microbial surface binding site concentration ( E 51 nM). V_max for Mn(II) oxidation agrees with the rates calculated from the value of the flux of Mn(II) to the oxidizing zone using the Mn(II) gradient and estimates of the eddy diffusion coefficient. This consistancy verifies our methodology and indicates that the rate of Mn(II) oxidation is nearly equal to the (V_max for the reaction. We conclude that in this environment the Mn(II) oxidation rate is more a function of the total number of surface binding sites than the Mn(H) concentration.Contribution #1601 from the School of Oceanography, Univ. of Washingtoncorresponding author     

NO serves as a signaling intermediate downstream of H2O2 to modulate dynamic microtubule cytoskeleton during responses to VD-toxins in Arabidopsis

Although hydrogen peroxide (H₂O₂) and nitric oxide (NO) can act as an upstream signaling molecule to modulate the dynamic microtubule cytoskeleton during the defense responses to Verticillium dahliae (VD) toxins in Arabidopsis, it is not known the relationship between these two signaling molecules. Here, we show that VD-toxin-induced NO accumulation was dependent on prior H₂O₂ production, NO is downstream of H₂O₂ in the signaling process, and that H₂O₂ acted synergistically with NO to modulate the dynamic microtubule cytoskeleton responses to VD-toxins in Arabidopsis.     

Tidal effects on the organic carbon mineralization rate under aerobic conditions in sediments of an intertidal estuary

Laboratory experiments and field measurements were conducted to examine the effect of tide on the organic carbon mineralization rate in sediments under aerobic conditions of an intertidal estuary. Core samples of surface sediments were collected from an intertidal estuary of the Kurose River, Hiroshima, Japan. To mimic low and high tide in the intertidal estuary, organic carbon mineralization rates in the samples were measured in the laboratory under both air-exposed and submerged conditions. Mineralization rates under air-exposed conditions were two to five times higher than those under submerged conditions. Field measurements of the rate of CO₂ emission from the sediment surface revealed a rapid increase in the rate as the sea level fell during ebb tide. The estimated amount of daily organic carbon mineralization assuming a constantly submerged condition was 30% less than that estimated when considering the semi-diurnal fluctuation in sea level. These results indicate that tide has a marked impact on the organic carbon mineralization rate in sediments under aerobic conditions on an intertidal estuary, and tidal effects need to be considered when the amount of mineralized organic carbon is estimated.     

A Reinvestigation of the Reaction of Desferrioxamine with Superoxide Radicals. A Pulse Radiolysis Study

The reaction of desferrioxamine with superoxide has been studied using the pulse radiolysis technique. The decay of O₂^- was not accelerated in the presence of up to 4 × 10^-4 M desferrioxamine at physiological pH. The rate constant was found to be lower than 2 × 10⁴ M^-1 S^-1. In acid solutions the rate constant of the reaction between desferrioxamine and HO₂ was found to be lower than 10₅ M^-1 S^-1. The reaction was not studied in alkaline solutions due to the high absorbance of desferrioxamine in the U. V. region. The pK of desferrioxamine was determined to be 9.2 ± 0.05.     

Oriented solids as a colloid suspension in nematic liquid crystal – New tool for IR-spectroscopic and structural elucidation of inorganic compounds and glasses

Possibilities of the linear-polarized infrared (IR-LD) spectroscopy of oriented colloid suspensions in nematic liquid crystals, for structural and local structural elucidation for first time are demonstrated of inorganic compounds and glasses. The advantages of the method for tellurite and borate glasses are shown. The IR-band assignment of the typical local structural units in the glasses are proposed by a comparison with the IR-characteristics of appropriate crystalline analogues as α-TeO₂, V₂O₅, MoO₃ · H₂O and its high temperature form. The IR-spectroscopic characteristics of BO₃, BO₄ and boroxol ring are elucidated, using crystalline β-BaB₂O₄, SrB₄O₇, H₃BO₃ and B₂O₃ as model systems, where the structural moieties have been refined by single crystal X-ray diffraction.     

A kinetic study on iron stimulation of the xanthine oxidase dependent oxidation of ascorbate

Xanthine oxidase reduces molecular oxygen to H₂O₂ and superoxide radicals during its catalytic action on xanthine, hypoxanthine or acetaldehyde. Ascorbate is catalytically oxidized by the superoxide radicals generated, when present in the reaction solution (Nishikimi 1975). The present study shows that iron ions markedly stimulate the enzyme dependent ascorbate oxidation, by acting as a red/ox-cycling intermediate between the oxidase and ascorbate. An apparent K_m-value of 10.8 M characterized the iron stimulatory effect on the reaction at pH 6.0. Reduced transition-state metals can be oxidized by H₂O₂ through a Fenton-type reaction. Catalase was found to reduce the effect of iron on the enzyme dependent ascorbate oxidation, strongly suggesting that H₂O₂, produced during catalysis, is involved in the oxidation of ferrous ions.     

Respiration and oxygen transport functions of the blood from an intertidal fish,Helcogramma medium (Tripterygiidae)

Synopsis Aquatic and aerial oxygen uptake (̇O₂), ventilation frequency, and oxygen transport properties of the blood were determined for the intertidal fish Helcogramma medium. Ventilation frequency increased in response to decreased environmental PO₂ and aquatic ̇O₂ was maintained down to a critical PO₂ of 30–40 mm Hg. Below PO₂ 30 mm Hg fish intermittently gulped air and finally emerged into air at PO₂ 18 mm Hg. After 1 h exposure to air ̇O₂ decreased to 60% of the aquatic rate and this was accompanied by an increase in blood lactate. Aerobic expansibility was reduced in air (×1.2) compared to water (× 5.5). The Hb concentration was 0.47 ± 0.13 mmol 1^–1 and hematocrit 11.55 ± 3.61% indicating a moderate O₂-carrying capacity. Oxygen affinity was not especially high (P₅₀ = 19 mm Hg at pH 7.7 and 15°C) and ATP was the predominant acid-soluble phosphate regulating P₅₀. The equilibrium curve was essentially hyperbolic (Hill's n = 1.2) with a marked Bohr effect = –1.06) and Root effect (saturation depressed by 50% at pH7.1). The pattern of respiration and the respiratory properties of the blood together with observations of the behaviour of the fish during aerial exposure indicated that Helcogramma is adapted to living in a well-aerated environment yet can adequately tolerate short term exposure to low aquatic PO₂ or air.     

Subcutaneous injection of interleukin 12 induces systemic inflammatory responses in humans: implications for the use of IL-12 as vaccine adjuvant

Interleukin 12 (IL-12) is a cytokine with important regulatory functions bridging innate and adaptive immunity. It has been proposed as an immune adjuvant for vaccination therapy of infectious diseases and malignancies. The inflammatory properties of IL-12 play an important role in the adjuvant effect. We studied the effect of s.c. injections of recombinant human IL-12 (rHuIL-12) in 26 patients with renal cell cancer and demonstrated dose-dependent systemic activation of multiple inflammatory mediator systems in humans. rHuIL-12 at a dose of 0.5 g/kg induced degranulation of neutrophils with a significant increase in the plasma levels of elastase (p<0.05) and lactoferrin (p=0.01) at 24 h. Additionally, rHuIL-12 injection mediated the release of lipid mediators, as demonstrated by a sharp increase in the plasma secretory phospholipase A₂ (sPLA₂) level (p=0.003). rHuIL-12, when administered at a dose of 0.1 g/kg, showed minimal systemic effects. In conclusion, when IL-12 is used as an adjuvant, doses should not exceed 0.1 g/kg, in order to avoid severe systemic inflammatory responses.     

Molecular dynamics simulations reveal initial structural and dynamic features for the A2AR as a result of ligand binding

G-protein-coupled receptors (GPCRs) are membrane proteins that have a wide variety of physiological roles. Adenosine receptors belong to the GPCR family. Adenosine receptors are implicated in many physiological disorders, such as Parkinson's disease, Huntington's disease, inflammatory and immune's disease and many others. Interestingly, crystal structures of the active and inactive conformations of the A₂-subtype adenosine receptor (A₂AR) have been solved. These two structures could be used to get insights about the conformational changes that occur during the process of activation/inactivation processes of this receptor. Therefore, two ligand-free simulations of the native active (PDB code: 3QAK) and inactive (PDB code: 3EML) conformations of the A₂AR and two halo-simulations were carried out to observe the initial conformational changes induced by coupling adenosine to the inactive conformation and caffeine to the active conformation. Furthermore, we constructed an A₂AR model that contained four thermostabilising mutations, L48A, T65A, Q89A and A54L, which had previously been determined to stabilise the bound conformation of the agonist, and we ran molecular dynamics simulations of this mutant to investigate how these point mutations might affect the inactive conformation of this receptor. This study provides insights about the initial structural and dynamic features that occur as a result of the binding of caffeine and adenosine in the active and inactive A₂AR structures, respectively, as well as the introduction of some mutations on the inactive structure of the A₂AR. Moreover, we provide useful and detailed information regarding structural features such as toggle switch and ionic lock during the activation/inactivation processes of this receptor.     

Butyrylcholinesterase is present in the human epidermis and is regulated by H2O2: more evidence for oxidative stress in vitiligo

The human epidermis holds the capacity for autocrine cholinergic signal transduction, but the presence of butyrylcholinesterase (BchE) has not been shown so far. Our results demonstrate that this compartment transcribes a functional BchE. Its activity is even higher compared to acetylcholinesterase (AchE). Moreover, we show that BchE is subject to regulation by H(2)O(2) in a concentration-dependent manner as it was recently described for AchE. Epidermal BchE protein expression and enzyme activities are severely affected by H(2)O(2) in vitiligo as previously demonstrated for AchE. Removal/reduction of H(2)O(2) by a pseudocatalase PC-KUS yields normal/increased protein expression and activities. H(2)O(2)-mediated oxidation of methionine residues in BchE was confirmed by FT-Raman spectroscopy. Computer simulation supported major alteration of the enzyme active site and its tetramerisation domain suggesting deactivation of the enzyme due to H(2)O(2)-mediated oxidation. Based on our results we conclude that H(2)O(2) is a major player in the regulation of the cholinergic signal via both AchE and BchE and this signal is severely affected in the epidermis of patients with active vitiligo.