Evaluating a new method to estimate the rate of leaf respiration in the light by analysis of combined gas exchange and chlorophyll fluorescence measurements

Day respiration (R(d)) is an important parameter in leaf ecophysiology. It is difficult to measure directly and is indirectly estimated from gas exchange (GE) measurements of the net photosynthetic rate (A), commonly using the Laisk method or the Kok method. Recently a new method was proposed to estimate R(d) indirectly from combined GE and chlorophyll fluorescence (CF) measurements across a range of low irradiances. Here this method is tested for estimating R(d) in five C(3) and one C(4) crop species. Values estimated by this new method agreed with those by the Laisk method for the C(3) species. The Laisk method, however, is only valid for C(3) species and requires measurements at very low CO(2) levels. In contrast, the new method can be applied to both C(3) and C(4) plants and at any CO(2) level. The R(d) estimates by the new method were consistently somewhat higher than those by the Kok method, because using CF data corrects for errors due to any non-linearity between A and irradiance of the used data range. Like the Kok and Laisk methods, the new method is based on the assumption that R(d) varies little with light intensity, which is still subject to debate. Theoretically, the new method, like the Kok method, works best for non-photorespiratory conditions. As CF information is required, data for the new method are usually collected using a small leaf chamber, whereas the Kok and Laisk methods use only GE data, allowing the use of a larger chamber to reduce the noise-to-signal ratio of GE measurements.     

Liquid chromatographic assay in plasma of one of the members of a new series of anticonvulsants: d,l-3-hydroxy-3-ethyl-3-phenylpropionamide

A method for the simultaneous determination of HEPP (d,l-3-hydroxy-3-ethyl-3-phenylpropionamide), a member of a new homologous series of phenylamide-derivative anticonvulsants, with six other antiepileptic drugs (ethosuximide, primidone, phenobarbital, phenytoin, carbamazepine and clonazepam) in plasma by high-performance liquid chromatography is described. These drugs are extracted from plasma by adding an equal volume of acetonitrile. An aliquot of the extract is then injected on a reversed-phase column with a acetonitrile-methanol-phosphate buffer mobile phase. The total time required for the whole analytical process, including the plasma pretreatment and chromatography, is approximately 30 min. The assay method is simple, rapid and reproducible, and therefore considered suitable for routine use in clinical investigations monitoring HEPP simultaneously with common antiepileptic drugs.     

Liquid chromatographic assay in plasma of one of the members of a new series of anticonvulsants: d,l-3-hydroxy-3-ethyl-3-phenylpropionamide

A method for the simultaneous determination of HEPP (d,l-3-hydroxy-3-ethyl-3-phenylpropionamide), a member of a new homologous series of phenylamide-derivative anticonvulsants, with six other antiepileptic drugs (ethosuximide, primidone, phenobarbital, phenytoin, carbamazepine and clonazepam) in plasma by high-performance liquid chromatography is described. These drugs are extracted from plasma by adding an equal volume of acetonitrile. An aliquot of the extract is then injected on a reversed-phase column with a acetonitrile-methanol-phosphate buffer mobile phase. The total time required for the whole analytical process, including the plasma pretreatment and chromatography, is approximately 30 min. The assay method is simple, rapid and reproducible, and therefore considered suitable for routine use in clinical investigations monitoring HEPP simultaneously with common antiepileptic drugs.     

Calculating glucose fluxes during meal tolerance test: a new computational approach

A new calculation method is proposed to quantify the endogenous glucose production (EGP), the glucose appearance rate due to meal ingestion (R(a meal)), and the glucose disposal (R(d)) during a three-tracer study design. The method utilizes the maximum likelihood theory combined with a regularization method to achieve a theoretically coherent computational framework. The method uses the two-compartment formulation of the glucose kinetics. Instead of assuming smoothness of unlabeled and labeled glucose concentrations, the method assumes that the EGP, the R(a meal), and the fractional glucose clearance are smooth, increasing plausibility of their individual estimates. The method avoids transformation of the measurement errors, which may skew the estimates of the EGP, R(a meal), and R(d) with the traditional approach. Finally, the sequential nature of the calculations is replaced by calculating the EGP, R(a meal), and R(d) in "one go" to avoid the propagation of the errors from the EGP and R(a meal) into R(d). An example study is shown demonstrating the utility of the approach. A better performance of the new method is demonstrated in a simulation study.     

On the fidelity of deoxyribonucleic acid synthesis directed by chromatin-associated deoxyribonucleic acid polymerase beta

Accuracy of poly[d(A-T)] synthesis catalyzed by chromatin-bound deoxyribonucleic acid (DNA) polymerase beta was measured with several types. A new procedure was developed for the isolation of copied poly[d(A-T)] from chromatin DNA. This method involved in vitro copying of poly[d(A-T)] by native chromatin and subsequent selective fragmentation of chromatin by restriction nucleases, proteinase K, and heat denaturation. The fragmented natural DNA is then separated from the high molecular weight poly[d(A-T)] by gel filtration. The efficacy of DNA removal by this procedure was validated by cesium chloride gradient and nearest-neighbor analysis of the product of the reaction and by measurement of the fidelity of poly[d(A-T)] synthesis by Escherichia coli DNA Pol I contaminated with increasing amounts of DNA. Also, DNA polymerases dissociated from chromatin retain the same accuracy as that of native chromatin. Synthesis of poly[d(A-T)] by chromatin is catalyzed mainly by DNA polymerase-beta. By use of the described technique, we find that the fidelity of this reaction is exceptionally low; approximately one dGTP was incorporated for every thousand complementary nucleotides polymerized.     

Method for direct discrimination of intra- and intermolecular hydrogen bonds, and characterization of the G(:A):G(:A):G(:A):G heptad, with scalar couplings across hydrogen bonds

Discrimination of intra- and intermolecular hydrogen bonds in a symmetric multimer has not been accomplished yet, although such discrimination would provide a crucial basis for construction of the multimeric architecture of nucleic acids by NMR. We have developed a direct and unambiguous method for such discrimination involving the use of scalar couplings across hydrogen bonds. The method has been validated with a symmetric dimer of d(GGGCTTTTGGGC), for which the structure including both intra- and intermolecular hydrogen bonds was already reported. This has demonstrated that our method can clearly discriminate these two kinds of hydrogen bonds. Then, the method was applied to a symmetric dimer of d(GGAGGAGGAGGA) and has provided decisive information on its multimeric architecture. Additionally, the values for scalar couplings across hydrogen bonds for G:G and G:A base pairs in the G(:A):G(:A):G(:A):G heptad formed by d(GGAGGAGGAGGA) were determined for the first time. This determination has provided an insight into the nature of the heptad.     

Structured illumination microscopy with interleaved reconstruction (SIMILR)

Structured illumination microscopy (SIM) is the commonly used super‐resolution (SR) technique for imaging subcellular dynamics. However, due to its need for multiple illumination patterns, the frame rate is just a fraction of that of conventional microscopy and is thus too slow for fast dynamic studies. A new SR image reconstruction method that maximizes the use of each subframe of the acquisition series is proposed for improving the super‐resolved frame rate by N times for N illumination directions. The method requires no changes in raw data and is appropriate for many versions of SIM setup, including those implementing fast illumination pattern generation mechanism based on spatial light modulator or digital micromirror device. The performance of the proposed method is demonstrated through imaging the highly dynamic endoplasmic reticulum where continuous rapid growths or shape changes of tiny structures are observed.      

Chemical synthesis of the 5'-terminal structure of U1 RNA

A new method for the synthesis of N2,N2-dimethylguanosine (DMG) is developed by reductive C-S bond cleavage by use of tributyltin hydride. An improved method for the synthesis of the key intermediate (1) for construction of the 5'-terminal structure of U1 RNA, which has a trimethylated cap (TMG) structure at its 5' end, is also described. By the use of 1, several TMG-capped ribonucleosides and oligonucleotides were synthesized.     

Rapid method for isolation and screening of cytochrome c oxidase-deficient mutants of Saccharomyces cerevisiae

We describe here a new method for the specific isolation of cytochrome c oxidase-deficient mutants of Saccharomyces cerevisiae. One unique feature of the method is the use of tetramethyl-p-phenylenediamine as a cytochrome c oxidase activity stain for yeast colonies. The staining of yeast colonies by tetramethyl-p-phenylenediamine is dependent upon a functional cytochrome c oxidase and is unaffected by other lesions in respiration. Since the tetramethyl-p-phenylenediamine colony staining reaction is rapid and simple, it greatly facilitates both the identification and characterization of cytochrome c oxidase-deficient mutants. Another feature of the method, which is made possible by the tetramethyl-p-phenylenediamine colony stain, is the use of an op1 parent strain for the isolation of nuclear pet or mitochondrial mit mutants in specific protein-coding genes. A parent strain that carries this marker selects against rho0 or rho- classes of pleiotropic respiratory-deficient mutants, since these are lethal in op1 strains. We have used this method to isolate 123 independently derived cytochrome c oxidase-deficient pet mutants and 300 independently derived mit mutants.     

The use of a high-throughput luminescent method to assess CYP3A enzyme induction in cultured rat hepatocytes

Assessment of a new chemical entity for cytochrome P450 (CYP) enzyme induction at an early stage in discovery is crucial to prevent potential drug-drug interactions. CYP3A, the most abundant CYP isoform in the liver, metabolizes approximately 50% of drugs currently on the market and is also a highly inducible enzyme. The use of both rat and human hepatocyte culture for the prediction of in vivo CYP3A induction has become refined and validated and is considered a standard in vitro model. The current evaluation of CYP3A enzyme induction involves the use of substrates requiring subsequent analysis of metabolites by high-performance liquid chromatography/mass spectrometry, which adds considerable time and cost. In the present study, we describe the use of a novel luminogenic substrate, luciferin-6'-pentafluoro-benzyl ether (PFBE), which allows for a fast and selective measurement of CYP3A enzyme induction in cultured rat hepatocytes. The extent of induction was evaluated using cells treated for 3 d with the prototypical inducers, dexamethasone, phenobarbital, and pregnenolone 16 alpha-carbonitrile (PCN). Enzyme activity was measured in the treated cells either by the depentafluorobenzylation of luciferin-PFBE or the testosterone 6-beta-hydroxylation. Using both methods, dexamethasone and PCN-treated cells exhibited strong CYP3A activity, whereas phenobarbital treatment resulted in a weak response. The fold induction varied between both methods, but this variability can be controlled by normalizing data from each treatment to a positive control. The results indicate that luciferin-PFBE is an attractive alternative to the use of conventional substrate, testosterone, providing a sensitive, robust, and rapid method compatible with the multiwell plate format for the assessment of CYP3A induction.     

Absorption mode two-dimensional NOE spectroscopy of exchangeable protons in oligonucleotides

A new NMR method is described for the generation of absorption mode two-dimensional NOE spectra of oligonucleotides in H2O solution. The method yields spectra that are free of baseline distortions with excellent suppression of the intense H2O resonance. The method is demonstrated for a sample of the dodecamer d(CGCGAATTCGCG)2. All exchangeable base protons are identified and a number of new types of NOE connectivities are observed.     

Solving group technology problems via clique partitioning

This paper presents a new clique partitioning (CP) model for the Group Technology (GT) problem. The new model, based on a novel 0/1 quadratic programming formulation, addresses multiple objectives in GT problems by drawing on production relationships to assign differing weights to machine/part pairs. The use of this model, which is readily solved by a basic tabu search heuristic, is illustrated by solving 36 standard test problems from the literature. The efficiency of our new CP model is further illustrated by solving three large scale problems whose linear programming relaxations are much too large to be solved by CPLEX. An analysis of the quality of the solutions produced along with comparisons made with other models and methods highlight both the attractiveness and robustness of the proposed method.     

An enzymatic glycosylation of nucleoside analogues using β-galactosidase from Escherichia coli

A new enzymatic method for the synthesis of β-galactosides of nucleosides and acyclic nucleoside analogues has been developed, using β-galactosidase from Escherichia coli as a catalyst and lactose as a sugar donor. The method is very rapid, feasible and last but not least inexpensive. Its applicability has been proven for a broad variety of possible substrates with respect to its scaling up for preparative use. Five new compounds from a series of nucleoside and acyclic nucleoside analogues have been prepared on a scale of several hundred milligrams, in all cases revealing very good results of the method concerning the reproducibility of the reaction yields and simplicity of the purification process.     

聚合酶链式反应快速鉴定啤酒有害菌研究

建立了PCR快速鉴定啤酒有害菌的新方法。用基于抗酒花基因horA部分序列的特异引物对啤酒污染乳酸菌进行PCR检测,灵敏度可达到3个细胞(CFU),样品的预培养需12~16h。啤酒有害菌检测所需时间从传统的5d减少到24h。     

A novel and simple method for quantification of small,dense LDL

A preponderance of small, dense (sd) LDL is strongly associated with the development of coronary heart disease, but the method for the measurement of sd LDL is too laborious for clinical use. We report a simple method for the quantification of sd LDL that is applicable to an autoanalyzer. This method consists of two steps: first, to precipitate the lipoprotein of density (d) <1.044 g/ml using heparin-magnesium; and second, to measure LDL-cholesterol in the supernatant by the homogeneous method or apolipoprotein B (apoB) by an immunoturbidometric assay. The cholesterol and apoB values obtained by the precipitation method (45 +/- 26 and 33 +/- 20 mg/dl, respectively) were similar to those obtained in the lipoprotein (d = 1.044-1.063) separated by ultracentrifugation (42 +/- 22 and 31 +/- 17 mg/dl, respectively), and there was an excellent correlation between the two methods for sd LDL-cholesterol (y = 1.05X + 1, r = 0.88, n = 69) and apoB (y = 1.07X, r = 0.90). Sd LDL values had a significant inverse correlation with LDL size. A high correlation was found between sd LDL-cholesterol and apoB values (r = 0.94). Sd LDL value was related to triglyceride, apoB, and LDL-cholesterol, but not to the buoyant LDL level. These results suggest that this precipitation method is a simple and rapid method for the measurement of sd LDL concentration.     

Electrophoretic mobility of high-molecular-weight, double-stranded DNA on agarose gels.

A new theoretical model for the migration of high-molecular-weight, double-stranded DNA on agarose gels is presented. This leads to the prediction that under certain conditions of electrophoresis, a linear relationship will exist between the molecular weight of a DNA molecule, raised to the (-2/3) power, and its electrophoretic mobility. Agarose gel electrophoresis of the fragments of bacteriophage lambda DNA produced by several restriction endonucleases confirms this relationship, and establishes some of the limits on its linearity. For this work, a polyacrylamide slab gel apparatus was modified for use with agarose gels. This apparatus has several advantages over others commercially available for agarose gel electrophoresis, including the abilities to run a larger number of samples at one time, to use lower-concentration gels, and to maintain better temperature stability across the width of the gel. The validation of the relationship developed here between molecular weight and electrophoretic mobility should make this a useful method for determining the molecular weights of DNA fragments.     

Maximizing productivity of CHO cell-based fed-batch culture using chemically defined media conditions and typical manufacturing equipment

A highly productive chemically defined fed-batch process was developed to maximize titer and volumetric productivity for Chinese hamster ovary cell-based recombinant protein manufacturing. Two cell lines producing a recombinant antibody (cell line A) and an Fc-fusion protein (cell line B) were used for development. Both processes achieved product titers of 10 g/L on day 18 under chemically defined conditions. For cell line B, the use of plant derived hydrolysates combined with the optimized chemically defined medium increased the titer to 13 g/L. Volumetric productivities were increased from a base line of about 200 mg/L/d to about 500 mg/L/d under chemically defined conditions and as high as 700 mg/L/d with cell line B using plant derived hydrolysates. Peak cell densities reached greater than 20E6 vc/mL, and cell viabilities were maintained above 80% on day 18 without the use of antiapoptotic genes or temperature shift. A rapid compound screening method was developed to effectively test positive factors within 72 h. Peak volumetric oxygen uptake rates (OUR) more than tripled from the baseline condition. Oxygen demand continued to increase after maximum cell density was reached with a maximal OUR of 3.7 mmol/L/h. The new process format was scaled up and verified at 100 L pilot scale using reactor equipment of similar configuration as used at manufacturing scale.     

Feedback control of human metabolic work rate during robotics-assisted treadmill exercise

A novel approach is presented which suggests the use of human metabolic work rate to define and regulate exercise intensity during robotics-assisted treadmill training. The work describes the design and technical validation of the new method.A feedback structure is proposed which provides automatic regulation of metabolic work rate, in conjunction with an embedded feedback loop for volitional control of mechanical work rate. Human metabolic work rate was derived in real time from breath-by-breath measurements of oxygen uptake and carbon dioxide output.The results show that the feedback method provides close to nominal performance for square-wave and ramp reference tracking tasks and that good disturbance rejection properties are obtained. A collateral finding of this work is an estimate of 14.5% of the metabolic efficiency of robotics-assisted treadmill exercise.The use of feedback control of human metabolic work rate provides a direct measure of exercise intensity as perceived by the exercising human as it directly reflects the energy requirements of the working muscles. This complements previous approaches to guiding robotics-assisted treadmill training based on mechanical work rate, heart rate or oxygen uptake. The new approach based on metabolic work rate may have advantages in populations with compromised and widely varying exercise responses. This provides a new approach for driving and controlling active patient participation during robotics-assisted treadmill exercise.     

Synthesis of CpFe(CO)(L) complexes of hydantoin anions (Cp = eta5-C5H5, L = CO, PPh3), and the use of the 5,5-diphenylhydantoin anion complexes as tracers in the nonisotopic immunoassay CMIA of this antiepileptic drug.

As part of our ongoing development of the CMIA nonisotopic immunoassay method, in which the tracers are metal carbonyl complexes and detection is by Fourier transform infrared spectroscopy, we examined the potential use as tracers of the complexes CpFe(CO)2(5,5-diphenylhydantoin) 2d and CpFe(CO)(PPh3)(5, 5-diphenylhydantoin) 3. The present study involved the synthesis of a series of hydantoin complexes (2a-2d), in particular that of the derivative of 5,5-diphenylhydantoin 2d. The structure of 2d was confirmed by X-ray crystallography. The infrared analysis, establishing the position and intensity of the characteristic metal-carbonyl peaks of complexes 2d and 3 in the 1850-2200 cm-1 region, shows that measurement of the absorbance values of these characteristic peaks will permit quantitative analysis in the picomole range, the norm for routine use in immunoassay and thus suitable for use as CMIA tracers. Cross-reaction rates of these tracers with anti-DPH specific antibodies show that 2d and 3 are both recognized by anti-DPH antibodies (cross-reaction rates 43 and 20%, respectively). In developing a CMIA of DPH with these tracers, it was found that 3, with a single, intense band at 1977 cm-1, had very promising IR characteristics for use in multiassay CMIA, but probably owing to its relatively weak affinity for the antibodies, it was not possible to develop a CMIA for DPH using this tracer. Complex 2d, however, showed better recognition by the antibodies, and using this complex as a tracer, it was possible to develop a particularly sensitive monoassay of DPH by the CMIA method.