Measurement of the rate of hydrogen production by Clostridium butyricum using an amperometric method

Abstract The rate of production of hydrogen by Clostridium butyricum was measured using a modified oxygraph equipment. As an example of the application of the method, some results of the investigations on the effect of short-chain volatile fatty acids on the metabolism of the organism are shown.     

A method for measuring the oxygen consumption of intact cell monolayers

This report describes an open-air method for measuring the O(2) consumption (QO(2)) of intact monolayers of cultured cells. This method is based on Fick's second law of diffusion. It requires only a micromanipulator and a miniature O(2) electrode to measure the PO(2) gradient in the culture medium in the well. It was compared with the conventional oxygraph chamber method. Both methods gave the same value for QO(2) in freshly isolated rat type II cells: 166 +/- 15.3 nmol. h(-1). 10(6) cells(-1) for the open-air method and 151 +/- 11.6 nmol. h(-1). 10(6) cells(-1) for the oxygraph chamber method (n = 11 experiments). But the open-air method gave significantly larger values for QO(2) in cells cultured for 2 days (236 +/- 8.8 nmol. h(-1). 10(6) cells(-1)) than the oxygraph method (71 +/- 15.2 nmol. h(-1). 10(6) cells(-1); P < 0.001; n = 12 experiments). This suggests that the way cells are detached from their substratum to be placed in the oxygraph chamber affects their QO(2). The open-air method may be useful for studies on the metabolic properties of monolayers because the cells do not risk being damaged.     

Inhibition of vitamin K-dependent carboxylase by metal ions and metal complexes: a reassessment

The vitamin K-dependent enzymatic carboxylation of glutamyl residues in blood protein precursors and in synthetic peptides is inhibited in vitro by transition metal complexes. Some authors suggested it is a result of metal ions interaction with intermediary oxygenated species. Using an oxygraph we have observed increases in the rate of oxygen utilization in the carboxylating system containing reduced vitamin K after addition of some transition metal ions and complexes. Kinetic studies indicate that, although oxygen utilization is increased by the addition of Cu2+, Fe3+, and hematin, the initial rate of carboxylation is not affected. The rate of carboxylation rapidly decreases at oxygen concentrations below 50 microM and reaches zero when oxygen is depleted. UV spectroscopy revealed simultaneous acceleration of the conversion of vitamin K hydroquinone into the parent quinone. The magnitude of these effects, as well as carboxylation inhibition, depends on the oxidation potential of the complexed ion and its lipophilicity. Addition of stable Mn parallel ion, which has no inhibitory effect on carboxylation, does not increase the rate of oxygen utilization nor the hydroquinone oxidation. The results suggest that inhibition of carboxylation by transition metals is mainly due to depletion of the necessary components (oxygen, vitamin K hydroquinone) of the carboxylating system rather than quenching of activated, oxygen-containing intermediates.     

Liver mitochondrial respiratory functions decline with age

Human liver mitochondrial respiration rates in Chinese populations of various ages were assayed with an oxygraph. In this study, State 3 and State 4 respiration rates, respiratory control ratio (RCR), and ADP/O ratio were measured for 35 Chinese subjects of 31 to 76 years old. We found a significant negative correlation between age and respiratory control and ADP/O ratios tested. Moreover, the respiratory control and ADP/O ratios decreased with the increase of age. These findings suggest that a substantial fall in mitochondrial oxidative capacity in ageing liver may be an important contributor to the ageing process.     

Inhibition of prostaglandin H synthase–catalyzed cooxidation of diethylstilbestrol by α-naphthoflavone and β-naphthoflavone

Prostaglandin H synthase (PHS) has gained interest as a drugmetabolizing enzyme and has been shown to cooxidize and metabolically activate diethylstilbestrol (DES) in vitro. Both 7,8-benzoflavone (α-naphthoflavone, ANF) and 5,6-benzoflavone (β-naphthoflavone, BNF) have now been studied for their effects on PHS from ram seminal vesicle microsomes by means of several in vitro assays. The PHS-catalyzed cooxidation of DES, as measured by high-performance liquid chromatography (HPLC) analysis, is inhibited by BNF and ANF at micromolar concentrations, with median inhibitory concentrations (IC-50) of<20 and 40 μM, respectively. The oxidation of DES is inhibited whether it is initiated by arachidonic acid or by hydrogen peroxide, indicating that the benzoflavones inhibit PHS by a mechanism different from that of indomethacin. Monitoring of cyclooxygenase activity in an oxygraph also reveals an inhibition of PHS by BNF which depends only weakly on arachidonic acid concentration; inhibition by ANF is less pronounced under these conditions. Since PHS-catalyzed conversion of the benzoflavone compounds was detected under conditions permitting cooxidation, the inhibition of PHS by benzoflavones in vitro could either be a direct effect or possibly mediated via metabolites. Our data imply that ANF and BNF, in addition to their well-known role as modifiers of mixed-function oxidases, can affect the PHS-catalyzed metabolism of xenobiotics. This is discussed in the context of adverse effects caused by DES in vivo and in cell culture and must be taken into account when interpreting the modifying effect of benzoflavones on these endpoints.     

Oxygen evolution and the permeability of the outer envelope of isolated whole chloroplasts

A rapid oxygraph method of studying the permeability of the envelope of isolated chloroplasts was used. The outer envelope of aqueously isolated whole spinach (Spinacia oleracea L.) chloroplasts in buffer is readily permeable to 3-phosphoglyceric acid, which induces an immediate light dependent oxygen evolution. This light dependent oxygen evolution was completely eliminated by swelling these plastids in an osmotically dilute solution. Exogenous adenosine diphosphate, but not inorganic phosphate, strongly stimulated this oxygen evolution. This indicated that the chloroplast envelope is relatively permeable to adenosine diphosphate.

Oxygen evolution and swelling studies indicated that the chloroplast envelope is relatively impermeable to NADP and to ferredoxin.

A method is described whereby the percent of whole chloroplasts present in a chloroplast preparation may be rapidly estimated.

     

Electron transfer associated with oxygen activation in the B2 protein of ribonucleotide reductase from Escherichia coli

Each of the two beta peptides which comprise the B2 protein of Escherichia coli ribonucleotide reductase (RRB2) possesses a nonheme dinuclear iron cluster and a tyrosine residue at position 122. The oxidized form of the protein contains all high spin ferric iron and 1.0-1.4 tyrosyl radicals per RRB2 protein. In order to define the stoichiometry of in vitro dioxygen reduction catalyzed by fully reduced RRB2 we have quantified the reactants and products in the aerobic addition of Fe(II) to metal-free RRB2apo utilizing an oxygraph to quantify oxygen consumption, electron paramagnetic resonance to measure tyrosine radical generation, and M?ssbauer spectroscopy to determine the extent of iron oxidation. Our data indicate that 3.1 Fe(II) and 0.8 Tyr122 are oxidized per mol of O2 reduced. M?ssbauer experiments indicate that less than 8% of the iron is bound as mononuclear high spin Fe(III). Further, the aerobic addition of substoichiometric amounts of 57Fe to RRB2apo consistently produces dinuclear clusters, rather than mononuclear Fe(III) species, providing the first direct spectroscopic evidence for the preferential formation of the dinuclear units at the active site. These stoichiometry studies were extended to include the phenylalanine mutant protein (Y122F)RRB2 and show that 3.9 mol-equivalents of Fe(II) are oxidized per mol of O2 consumed. Our stoichiometry data has led us to propose a model for dioxygen activation catalyzed by RRB2 which invokes electron transfer between iron clusters.     

Measurement of 'in situ' mitochondrial membrane potential in Ehrlich ascites tumor cells during aerobic glycolysis

(1) A method is presented for continuous and simultaneous monitoring of the 'in situ' mitochondrial membrane potential (delta psi m) and respiration rate of Ehrlich ascites tumor cells. The method involves permeabilization of the plasma membrane, achieved by treatment with low digitonin concentration, and the use of a TPP+ selective electrode attached to an oxygraph vessel. Binding of the probe inside the cells was analyzed assuming a proportional relationship between the amount of bound TPP+ and the free concentration of the lipophilic cation. (2) Evidence is reported that the addition of glucose to digitonin-permeabilized Ehrlich ascites tumor cells causes a decrease of mitochondrial membrane potential that coincided with a transient enhancement of the respiration rate and remained unchanged during the subsequent Crabtree effect. We have characterized the effect of glucose on delta psi m by determining its dependent on the glycolytic pathway and its sensitivity towards oligomycin. The mutual relationships between glucose and ADP effects on the mitochondrial membrane potential were also studied. A plausible mechanism underlying the depolarization of mitochondrial membrane induced by glucose is presented.     

Kinetic properties of glycerophosphate oxidase isolated from dry baker's yeast

The glycerophosphate oxidase is a flavoprotein responsible for the catalysis of the oxidation of the glycerophosphate to dihydroxyacetone phosphate, through the reduction of the oxygen to hydrogen peroxide. The glycerophosphate oxidase from baker's yeast was specific for l-α-glycerol phosphate. It was estimated by monitoring the consumption of oxygen with an oxygraph. An increase of 32% in consumption of oxygen was obtained when the enzyme was concentrated 16-fold. The assay of enzyme was determined by the peroxidase chromogen method followed at 500 nm. The procedure for the standardization of the activity of the glycerophosphate oxidase from baker's yeast was accomplished, and the pH and temperature stability showed that the enzyme presented a high stability at pH 8.0, and the thermal stability was maintained up to 60 °C during 1 h. Such method allowed quantifying in the range 92–230 mM of glycerol phosphate, an important intermediate metabolite from lipid biosynthesis and glycolytic routes.     

The oxidation of arachidonic acid by the cyclooxygenase activity of purified prostaglandin H synthase: spin trapping of a carbon-centered free radical intermediate

The ESR spin trapping technique was used to study the first detectable radical intermediate in the oxidation of arachidonic acid by purified prostaglandin H synthase. The holoenzyme and the apoenzyme, reconstituted with either hematin or Mn2+ protoporphyrin IX, were investigated. Depending on the different types of enzyme activity present, arachidonic acid was oxidized to at least two free radicals. One of these radicals is thought to be the first ESR detectable radical intermediate in the conversion of arachidonic acid to prostaglandin G2 and was detected previously in incubations of ram seminal vesicle microsomes, which are rich in prostaglandin H synthase. The ESR findings correlated with oxygen incorporation into arachidonic acid and prostaglandin formation, where the spin trap inhibits oxygen incorporation and prostaglandin formation by apparently competing with oxygen for the carbon-centered radical. Substitution of arachidonic acid by octadeuterated (5, 6, 8, 9, 11, 12, 14, 15)-arachidonic acid confirmed that the radical adduct contained arachidonic acid that is bound to the spin trap at one of these eight positions. An attempt was made to explain the apparent time lag between the metabolic activity observed in the oxygraph measurements and the appearance of the trapped radical signals.     

Creatine kinase of heart mitochondria. Control of oxidative phosphorylation by the extramitochondrial concentrations of creatine and phosphocreatine

Defining how extramitochondrial high-energy phosphate acceptors influence the rates of heart oxidative phosphorylation is essential for understanding the control of myocardial respiration. When the production of phosphocreatine is coupled to electron transport via mitochondrial creatine kinase, the net reaction can be expressed by the balanced equation: creatine + Pi----phosphocreatine + H2O. This suggests that rates of oxygen consumption could be regulated by changes in [creatine], [Pi], or [phosphocreatine], alone or in combination. The effects of altering these metabolites upon mitochondrial rates of respiration were examined in vitro. Rat heart mitochondria were incubated in succinate-containing oxygraph medium (pH 7.2, 37 degrees C) supplemented with five combinations of creatine (1.0-20 mM), phosphocreatine (0-25 mM), and Pi (0.25-5.0 mM). In all cases, the mitochondrial creatine kinase reaction was initiated by additions of 0.5 mM ATP. To emphasize the duality of control, the results are presented as three-dimensional stereoscopic projections. Under physiological conditions, with 5.0 mM creatine, increases in Pi or decreases in phosphocreatine had little influence upon mitochondrial respiration. When phosphocreatine was held constant (15 mM), changes in [creatine] modestly stimulated respiratory rates, whereas Pi again showed little effect. With 1.0 mM Pi, respiration clearly became dependent upon changes in [creatine] and [phosphocreatine]. Initially, respiratory rates increased as a function of [creatine]. However, at [phosphocreatine] values below 10 mM, product "deinhibition" was observed, and respiratory rates rapidly increased to 80% State 3. With 2.0 mM Pi or higher, respiration could be regulated from State 4 to 100% State 3. Overall, the data show how increasing [creatine] and decreasing [phosphocreatine] influence the rates of oxidative phosphorylation when mediated by mitochondrial creatine kinase. Thus, these changes may become secondary cytoplasmic signals regulating heart oxygen consumption.     

Organizing research data

Research relies on ever larger amounts of data from experiments, automated production equipment, questionnaries, times series such as weather records, and so on. A major task in science is to combine, process and analyse such data to obtain evidence of patterns and correlations.Most research data are on digital form, which in principle ensures easy processing and analysis, easy long-term preservation, and easy reuse in future research, perhaps in entirely unanticipated ways. However, in practice, obstacles such as incompatible or undocumented data formats, poor data quality and lack of familiarity with current technology prevent researchers from making full use of available data.This paper argues that relational databases are excellent tools for veterinary research and animal production; provides a small example to introduce basic database concepts; and points out some concerns that must be addressed when organizing data for research purposes.     

Legislation for trial registration and data transparency

Sharing of final research data from clinical research is an essential part of the scientific method. The U.S. National Institutes of Health require some grant applications to include plans for sharing final research data, which it defines as the factual materials necessary to document, support, and validate research findings. In the U.S., however, the Privacy Rule adopted under the Health Insurance Portability and Accountability Act impedes the sharing of final research data. In most situations, final research data may be shared only where all information that could possibly be used to identify the subject has been deleted, or where the subject has given authorization for specific research, or an Institutional Review Board has granted a waiver.     

生物数据标准化研究进展

随着生物测序技术的快速发展,积累了海量的生物数据。生物数据资源作为生物分析研究及应用的核心和源头,为保证数据的正确性、可用性和安全性,对生物数据资源进行标准化的管理非常重要和迫切。本文综述了目前国内外生物数据标准化研制进展,目前国内外对生物数据缺少一个总体的规划,生物数据语义存在大量的不兼容性,数据格式多种多样,在生物数据收集、处理、存储和共享等方面缺乏统一的标准。国内外生物数据标准化处于起步阶段,但各国生物专家都在努力进行标准研制工作。文章最后从生物数据术语、生物数据资源收集、处理和交换、存储、生物数据库建设和生物数据伦理规范等方面出发,对标准研制工作进行一一探讨,期望能为生物数据标准制定提供一定的参考和依据。     

Reactivity of toluate dioxygenase with substituted benzoates and dioxygen

Toluate dioxygenase (TADO) of Pseudomonas putida mt-2 catalyzes the dihydroxylation of a broad range of substituted benzoates. The two components of this enzyme were hyperexpressed and anaerobically purified. Reconstituted TADO had a specific activity of 3.8 U/mg with m-toluate, and each component had a full complement of their respective Fe(2)S(2) centers. Steady-state kinetics data obtained by using an oxygraph assay and by varying the toluate and dioxygen concentrations were analyzed by a compulsory order ternary complex mechanism. TADO had greatest specificity for m-toluate, displaying apparent parameters of KmA = 9 +/- 1 microM, k(cat) = 3.9 +/- 0.2 s(-1), and K(m)O(2) = 16 +/- 2 microM (100 mM sodium phosphate, pH 7.0; 25 degrees C), where K(m)O(2) represents the K(m) for O(2) and KmA represents the K(m) for the aromatic substrate. The enzyme utilized benzoates in the following order of specificity: m-toluate > benzoate approximately 3-chlorobenzoate > p-toluate approximately 4-chlorobenzoate > o-toluate approximately 2-chlorobenzoate. The transformation of each of the first five compounds was well coupled to O(2) utilization and yielded the corresponding 1,2-cis-dihydrodiol. In contrast, the transformation of ortho-substituted benzoates was poorly coupled to O(2) utilization, with >10 times more O(2) being consumed than benzoate. However, the apparent K(m) of TADO for these benzoates was >100 microM, indicating that they do not effectively inhibit the turnover of good substrates.     

YOU CAN USE MY NAME; YOU DON'T HAVE TO STEAL MY STORY – A CRITIQUE OF ANONYMITY IN INDIGENOUS STUDIES

Our claim in this paper is that not being identified as the data source might cause harm to a person or group. Therefore, in some cases the default of anonymisation should be replaced by a careful deliberation, together with research subjects, of how to handle the issues of identification and confidentiality. Our prime example in this article is community participatory research and similar endeavours on indigenous groups. The theme, content and aim of the research, and the question of how to handle property rights and ownership of research results, as well as who should be in charge of the research process, including the process of creating anonymity, should all be answered, before anonymity is accepted.     

Virtual Reality: Beyond Visualization

Virtual reality (VR) has recently become an affordable technology. A wide range of options are available to access this unique visualization medium, from simple cardboard inserts for smartphones to truly advanced headsets tracked by external sensors. While it is now possible for any research team to gain access to VR, we can still question what it brings to scientific research. Visualization and the ability to navigate complex three-dimensional data are undoubtedly a gateway to many scientific applications; however, we are convinced that data treatment and numerical simulations, especially those mixing interactions with data, human cognition, and automated algorithms will be the future of VR in scientific research. Moreover, VR might soon merit the same level of attention to imaging data as machine learning currently has. In this short perspective, we discuss approaches that employ VR in scientific research based on some concrete examples.     

利用遥感技术实现作物模拟模型区域应用的研究进展

作物模拟模型从单点发展到区域应用时,模型中一些宏观资料的获取和参数的区域化方面出现困难,利用遥感技术将实现作物模拟模型的区域应用．文中综述了近年来遥感反演作物模型所需的地表生物物理参数的方法、利用遥感信息直接获取生物量的途径和遥感信息与作物模拟模型之间时空匹配问题等方面的研究概况,重点介绍了利用遥感技术实现作物模拟模型区域应用的3种解决方案(强迫型、调控型和验证型)及其研究进展,并讨论了目前存在的问题和今后研究的方向．     

Plains History and Cultural Anthropology

Abstract

Recent cutbacks in research funding and the burgeoning population of anthropology graduate departments may soon force cultural anthropologists to recognize what their archaeological colleagues have long known: their own “backyard” is a field for fertile research. Specifically, cultural anthropologists may turn increasingly to using long-neglected data sources - rich in documentation - on Anglo-Saxon America. This paper briefly investigates some reasons for the study of American historical data and presents a preliminary analysis of some data.