Profound difference of metabolic pharmacokinetics between pure glycyrrhizin and glycyrrhizin in licorice decoction

To investigate the difference of metabolic pharmacokinetics between pure glycyrrhizin (GZ) and GZ in licorice decoction, six New Zealand White rabbits were orally given pure GZ and licorice decoction containing equivalent content of GZ in a randomized crossover design. HPLC methods were used for the quantitation of GZ and glycyrrhetic acid (GA) in serum. The results indicated that the areas under curves (AUCs) of GZ and GA after administration of licorice decoction were significantly higher than those after pure GZ. This result was contradictory with that obtained in rats. To explore the mechanism of the pharmacokinetic difference, feces of rabbits, rats, pigs and humans were used to investigate the presystemic metabolism of pure GZ and GZ in licorice decoction. The results indicated that pure GZ was hydrolyzed to GA more rapidly and to a greater extent than that in licorice decoction by various feces. In addition, when pure GZ was fermented, the metabolic profiles of GA and 3-dehydroGA in rabbit feces were quite different from other feces. In conclusion, the bioavailabilities of GZ and GA are significantly better from licorice than from pure GZ in rabbits but the presystemic metabolism of pure GZ in rabbit is rather different from that in rat, pig and human.     

Newly discovered orally active pure antiestrogens

In order to develop orally active pure antiestrogens, we incorporated the carboxy-containing side chains into the 7alpha-position of the steroid scaffold and found that 17-keto derivative CH4893237 (12b) functioned as a pure antiestrogen with its oral activity much superior to clinically used pure antiestrogen, ICI182,780. Results from the pharmacokinetic evaluation indicated that the potent antiestrogen activity at oral dosing in mice attributed to both improved absorption from the intestinal wall and metabolic stability in liver.     

A comparison of vessel sensitivity and vessel constant in oxygen uptake determination with pure oxygen and air as gaseous media.

Air proved to be a superior gaseous medium to pure oxygen used for oxygen uptake study in the Warburg apparatus Recording of volume change (vessel sensitivity method) was the only correct method of recording the oxygen uptake. It is concluded that the volume change method should be followed for recording oxygen uptake by Warburg apparatus and pure oxygen should not be used as a gaseous medium.     

A hidden-state Markov model for cell population deconvolution.

Microarrays measure gene expression typically from a mixture of cell populations during different stages of a biological process. However, the specific effects of the distinct or pure populations on measured gene expression are difficult or impossible to determine. The ability to deconvolve measured gene expression into the contributions from pure populations is critical to maximizing the potential of microarray analysis for investigating complex biological processes. In this paper, we describe a novel approach called the multinomial hidden Markov model (MHMM) that produces: (i) a maximum a posteriori estimate of the fraction represented by each pure population and (ii) gene expression values for each pure population. Our method uses an unsupervised, probabilistic approach for handling missing data points and clusters genes based on expression in pure populations. MHMM, used with several yeast datasets, identified statistically significant temporal dynamics. This method, unlike the linear decomposition models used previously for deconvolution, can extract information from different types of data, does not require a priori identification of pure gene expression, exploits the temporal nature of time series data, and is less affected by missing data.     

鱼肝线粒体DNA的简易提纯方法

本文报道一种简易分离纯化线粒体DNA(mtDNA)的方法。即以差速离心或蔗糖梯度离心制得线粒体后,用RNase除去RNA,可得纯mtDNA,或用凝胶过滤、或低熔点琼脂糖法纯化之。所获纯mtDNA可用于限制性酶切图谱的组建和其片段的克隆。此法可避开冗长的昂贵的超速离心,故可为普通实验室所采用。文中还讨论了mtDNA纯化和得率的因素。     

Weight calibration to improve the efficiency of pure risk estimates from case-control samples nested in a cohort

Cohort studies provide information on relative hazards and pure risks of disease. For rare outcomes, large cohorts are needed to have sufficient numbers of events, making it costly to obtain covariate information on all cohort members. We focus on nested case-control designs that are used to estimate relative hazard in the Cox regression model. In 1997, Langholz and Borgan showed that pure risk can also be estimated from nested case-control data. However, these approaches do not take advantage of some covariates that may be available on all cohort members. Researchers have used weight calibration to increase the efficiency of relative hazard estimates from case-cohort studies and nested cased-control studies. Our objective is to extend weight calibration approaches to nested case-control designs to improve precision of estimates of relative hazards and pure risks. We show that calibrating sample weights additionally against follow-up times multiplied by relative hazards during the risk projection period improves estimates of pure risk. Efficiency improvements for relative hazards for variables that are available on the entire cohort also contribute to improved efficiency for pure risks. We develop explicit variance formulas for the weight-calibrated estimates. Simulations show how much precision is improved by calibration and confirm the validity of inference based on asymptotic normality. Examples are provided using data from the American Association of Retired Persons Diet and Health Cohort Study.     

Commensalism during submerged mixed culture of Geotrichum candidum and Penicillium camembertii on glutamate and lactate

Geotrichum candidum and Penicillium camembertii were cultivated in pure and mixed cultures on glutamate- and lactate-based medium. In pure culture, P. camembertii assimilated simultaneously glutamate, as a nitrogen and carbon source for biosynthesis, and lactate as an energy source. On the contrary, G. candidum grew on glutamate alone. The mixed culture led to higher growth rates and then higher rates of substrate consumption and metabolite production than each pure culture; however, the behaviour recorded was similar to that observed during G. candidum pure culture, in particular the absence of lactate assimilation during growth, illustrating a commensalism between both species. The presence of G. candidum induced a form of “competition” and then a better assimilation by P. camembertii of the sole nitrogen source, glutamate, which was therefore used as an energy source in addition to be a carbon (and nitrogen) source. Lactate was only used for energy supply during stationary state, as also recorded during G. candidum pure culture.     

Very pure porcine insulin in clinical practice.

In a one-year follow-up study the insulin dose in diabetic patients using very pure porcine insulin was compared with that in patients using conventional preparations. The dose of insulin used to obtain diabetic control was reduced by 7% in 108 patients treated solely with very pure porcine insulin from the start of insulin treatment when compared with 108 matched patients who had received conventional insulins. In 117 patients whose treatment had been changed from conventional bovine or bovine-porcine insulin to very pure porcine insulin the dose was reduced by 9%. A further 511 patients receiving conventional insulins were examined for local cutaneous or subcutaneous abnormalities at insulin injection sites. Lipoatrophy was found in 49 of these patients (10%), but not in patients using very pure porcine insulin. The results confirm that very pure porcine insulin reduces the insulin dose needed to maintain diabetic control and may resolve or prevent local reactions such as lipoatrophy. Long-term advantages in reduced antigenicity to insulin and contaminating peptides remain to be established.     

Comparing the dehalogenase gene pool in cultivated alpha-halocarboxylic acid-degrading bacteria with the environmental metagene pool

Culture-dependent and culture-independent approaches were used to determine the relationship between the dehalogenase gene pool in bacteria enriched and isolated on 2,2-dichloropropionic acid (22DCPA) and the environmental metagene pool (the collective gene pool of both the culturable and uncultured microbes) from which they were isolated. The dehalogenases in the pure-cultures isolates, which were able to degrade 22DCPA, were similar to previously described group I and II dehalogenases. Significantly, the majority of the dehalogenases isolated from activated sludge by degenerate PCR with primers specific for alpha-halocarboxylic acid dehalogenases were not closely related to the dehalogenases in any isolate. Furthermore, the dehalogenases found in the pure cultures predominated in the enrichments but were a minor component of the community used to inoculate the batch cultures. Phylogenetic analysis of the dehalogenase sequences isolated by degenerate PCR showed that the diversity of the group II deh gene was greater than that of the group I deh gene. Direct plating of the activated sludge onto minimal media supplemented with 22DCPA resulted in biomass and DNA from which dehalogenases were amplified. Analysis of the sequences revealed that they were much more closely related to the sequences found in the community used to start the enrichments. However, no pure cultures were obtained with this isolation method, and thus no pure cultures were available for identification. In this study we examined the link between genes found in pure cultures with the metagene pool from which they were isolated. The results show that there is a large bias introduced by culturing, not just in the bacteria isolated but also the degradative genes that they contain. Moreover, our findings serve as a caveat for studies involving the culturing of pure cultures of bacteria and conclusions which are drawn from analysis of these organisms.     

Comparing the Dehalogenase Gene Pool in Cultivated α-Halocarboxylic Acid-Degrading Bacteria with the Environmental Metagene Pool

Culture-dependent and culture-independent approaches were used to determine the relationship between the dehalogenase gene pool in bacteria enriched and isolated on 2,2-dichloropropionic acid (22DCPA) and the environmental metagene pool (the collective gene pool of both the culturable and uncultured microbes) from which they were isolated. The dehalogenases in the pure-cultures isolates, which were able to degrade 22DCPA, were similar to previously described group I and II dehalogenases. Significantly, the majority of the dehalogenases isolated from activated sludge by degenerate PCR with primers specific for α-halocarboxylic acid dehalogenases were not closely related to the dehalogenases in any isolate. Furthermore, the dehalogenases found in the pure cultures predominated in the enrichments but were a minor component of the community used to inoculate the batch cultures. Phylogenetic analysis of the dehalogenase sequences isolated by degenerate PCR showed that the diversity of the group II deh gene was greater than that of the group I deh gene. Direct plating of the activated sludge onto minimal media supplemented with 22DCPA resulted in biomass and DNA from which dehalogenases were amplified. Analysis of the sequences revealed that they were much more closely related to the sequences found in the community used to start the enrichments. However, no pure cultures were obtained with this isolation method, and thus no pure cultures were available for identification. In this study we examined the link between genes found in pure cultures with the metagene pool from which they were isolated. The results show that there is a large bias introduced by culturing, not just in the bacteria isolated but also the degradative genes that they contain. Moreover, our findings serve as a caveat for studies involving the culturing of pure cultures of bacteria and conclusions which are drawn from analysis of these organisms.     

Computation Confirms Contraction: A Molecular Dynamics Study of Liquid Methanol,Water and a Methanol-Water Mixture

It may be questioned whether potential models that have been developed independently for two different pure compounds would behave properly when used in computer simulations of mixtures of these compounds. Since they are optimized for the pure compounds there is no guarantee whatsoever that the terms describing the interaction between dissimilar molecules are correct. If the simulational and experimental values of several thermodynamical properties of the mixture relative to those of the pure compounds agree closely, however, this strongly indicates that no separate optimizations need be carried out for the mixtures. Here we present the results of isothermal-isobaric Molecular Dynamics simulations of liquid methanol, water and equimolar methanol-water mixtures, using simple point charge models. The potential parameters of the models for the pure liquids had been independently optimized. No adjustment of parameters was made for the mixture, but nonetheless the experimental volume contraction and excess enthalpy upon mixing were reproduced almost perfectly.     

Pure moment testing for spinal biomechanics applications: Fixed versus sliding ring cable-driven test designs

In vitro multi-axial bending testing using pure moment loading conditions has become the standard in evaluating the effects of different types of surgical intervention on spinal kinematics. Simple, cable-driven experimental set-ups have been widely adopted because they require little infrastructure. Traditionally, “fixed ring” cable-driven experimental designs have been used; however, there have been concerns with the validity of this set-up in applying pure moment loading. This study involved directly comparing the loading state induced by a traditional “fixed ring” apparatus versus a novel “sliding ring” approach. Flexion-extension bending was performed on an artificial spine model and a single cadaveric test specimen, and the applied loading conditions to the specimen were measured with an in-line multiaxial load cell. The results showed that the fixed ring system applies flexion-extension moments that are 50–60% less than the intended values. This design also imposes non-trivial anterior–posterior shear forces, and non-uniform loading conditions were induced along the length of the specimen. The results of this study indicate that fixed ring systems have the potential to deviate from a pure moment loading state and that our novel sliding ring modification corrects this error in the original test design. This suggests that the proposed sliding ring design should be used for future in vitro spine biomechanics studies involving a cable-driven pure moment apparatus.     

Different sensitivity of Ca(2+)-ATPase and cholinesterase to pure and commercial pesticides in nervous ganglia of Phyllocaulis soleiformis (Mollusca)

We measured the effects in vitro of pure and commercial pesticides on Ca(2+)-activated ATPase and cholinesterase (ChE) activities in the nervous system of the slug Phyllocaulis soleiformis. The pesticides used in this study included carbamate and organophosphates, which acts as reversible and irreversible anticholinesterases, respectively. Both enzymes were insensitive to pure carbofuran (1 mM), glyphosate (1 mM) and malathion (120 microM). However, the carbamate carbofuran, in the commercial formulation Furandan 350S, inhibited ATPase and ChE activities. The organophosphate glyphosate used in the commercial preparation of Gliz 480CS inhibited ATPase activity and increased cholinesterase activity. These effects are likely due to the action of adjuvant substances of the chemical formulation. The commercial formulation (Malatol 500CE) did not alter enzymes activities. Our results suggest that cholinesterase present in the slug nervous tissue has a different behavior to those identified in vertebrate nervous tissue, since it was insensitive to pure compounds, known as anticholinesterases in vertebrates. Considering the insensitivity of the Ca(2+)-activated ATPase, we suggested that the purinergic neurotransmission and other roles of ATP might not be affected by the pure pesticides tested.     

Characterization of Cu2+-binding modes in the prion protein by visible circular dichroism and multivariate curve resolution

Visible circular dichroism (CD) spectra from the copper(II) titration of the metal-binding region of the prion protein, residues 57-98, were analyzed using the self-modeling curve resolution method multivariate curve resolution-alternating least squares (MCR-ALS). MCR-ALS is a set of mathematical tools for estimating pure component spectra and composition profiles from mixture spectra. Model-free solutions (e.g., soft models) are produced under the assumption that pure component profiles should be nonnegative and unimodal. Optionally, equality constraints can be used when the concentration or spectrum of one or more species is known. MCR-ALS is well suited to complex biochemical systems such as the prion protein which binds multiple copper ions and thus gives rise to titration data consisting of several pure component spectra with overlapped or superimposed absorption bands. Our study reveals the number of binding modes used in the uptake of Cu²⁺ by the full metal-binding region of the prion protein and their relative concentration profiles throughout the titration. The presence of a non-CD active binding mode can also be inferred. We show that MCR-ALS analysis can be initialized using empirically generated or mathematically generated pure component spectra. The use of small model peptides allows us to correlate specific Cu²⁺-binding structures to the pure component spectra.     

A two-dimension otolith growth inverse model

An inverse growth model was developed to describe fish otolith ontogenetic growth to find the most parsimonious growth field that drives the actual shape of an internal incremental structure to the actual external shape of the otolith. This approach is based in a pure physic model, and the single implicit assumption was that the otolith accretion occurred perpendicular to its external surface. The model could be used to define a general hypothesis situation, in the sense that it predicts the most plausible shape of the otolith at any time, assuming that no additional external forces have acted. Therefore, severe departures between the observed growth structure and the closest prediction to it could be used to identify anatomical constraints and physiological factors that modulate the pure physical expectations.     

Preparation of magnetic resonance contrast agents activated by beta-galactosidase

The preparation of beta-EgadMe and alpha-EgadMe, magnetic resonance (MR) contrast agents that can be used for in vivo detection of beta-galactosidase, is described. Diastereomerically pure beta-EgadMe can be synthesized by kinetically resolving the starting material as described in Step 1. The total time for the preparation of the racemic mixture of beta-EgadMe is about 8 d, and the total time for an diastereomerically resolved agent is about 9 d. The final metallated agent is stable at room temperature as a solid or in aqueous buffer (pH 5.5-10) indefinitely. Diastereomerically pure alpha-EgadMe can be prepared by beginning the synthesis with enantiomerically pure bromopropionic acid. The total time for the preparation of racemic alpha-EgadMe or diastereomerically pure alpha-EgadMe is about 8 d. The final metallated agent is stable at room temperature as a solid or in aqueous buffer (pH 5.5-10) indefinitely.     

Methods to increase enantioselectivity of lipases and esterases

Lipases and esterases are frequently used in the synthesis of optically pure compounds; however, natural enzymes do not always show sufficiently high enantioselectivity. Variation of the structure of the substrates, modification of the reaction system or protein engineering (e.g. the expression of pure enzymes, rational design or directed evolution) are strategies that can be employed to improve the distinction between two enantiomers or enantiotopic groups.     

Thermophilic archaeal enzymes and applications in biocatalysis

Thermophilic enzymes have advantages for their use in commercial applications and particularly for the production of chiral compounds to produce optically pure pharmaceuticals. They can be used as biocatalysts in the application of 'green chemistry'. The thermophilic archaea contain enzymes that have already been used in commercial applications such as the L-aminoacylase from Thermococcus litoralis for the resolution of amino acids and amino acid analogues. This enzyme differs from bacterial L-aminoacylases and has similarities to carboxypeptidases from other archaeal species. An amidase/γ-lactamase from Sulfolobus solfataricus has been used for the production of optically pure γ-lactam, the building block for antiviral carbocyclic nucleotides. This enzyme has similarities to the bacterial signature amidase family. An alcohol dehydrogenase from Aeropyrum pernix has been used for the production of optically pure alcohols and is related to the zinc-containing eukaryotic alcohol dehydrogenases. A transaminase and a dehalogenase from Sulfolobus species have also been studied. The archaeal transaminase is found in a pathway for serine synthesis which is found only in eukaryotes and not in bacteria. It can be used for the asymmetric synthesis of homochiral amines of high enantioselective purity. The L-2-haloacid dehalogenase has applications both in biocatalysis and in bioremediation. All of these enzymes have increased thermostability over their mesophilic counterparts.     

杉木(Cunninghamia lanceolata)、火力楠(Michelia macclurei)纯林及其混交林细根分布、分解与养分归还

用土钻法研究了杉木（Ｃｕｎｎｉｎｇｈａｍｉａｌａｎｃｅｏｌａｔａ）、火力楠（Ｍｉｃｈｅｌｉａｍａｃｌｕｒｅｉ）纯林和混交林的细根分布,用分解袋法研究了杉木和火力楠细根的分解,计算了３个林分中细根分解的Ｎ,Ｐ,Ｋ,Ｃａ,Ｍｇ的归还量。活细根的垂直分布以火力楠纯林层次性最强,混交林次之,杉木纯林最差。火力楠细根的养分含量比杉木细根高,而Ｃ／Ｎ比低。火力楠细根年分解率比杉木快,火力楠为５７．７％,而杉木为３２．７８％。细根分解的养分归还量多少顺序依次为：火力楠纯林、杉木火力楠混交林和杉木纯林。混交林中,细根分解的Ｎ,Ｐ,Ｋ,Ｃａ和Ｍｇ归还量分别为枯枝落叶的３３．３８％,５．８２％,２６９．３３％,３４．１２％和３７６．０８％。细根在３个林分的物质循环和周转中起着不可忽视的作用。     

Maximizing crossbred performance through purebred genomic selection

Background

In livestock production, many animals are crossbred, with two distinct advantages: heterosis and breed complementarity. Genomic selection (GS) can be used to select purebred parental lines for crossbred performance (CP). Dominance being the likely genetic basis of heterosis, explicitly including dominance in the GS model may be an advantage to select purebreds for CP. Estimated breeding values for CP can be calculated from additive and dominance effects of alleles that are estimated using pure line data. The objective of this simulation study was to investigate the benefits of applying GS to select purebred animals for CP, based on purebred phenotypic and genotypic information. A second objective was to compare the use of two separate pure line reference populations to that of a single reference population that combines both pure lines. These objectives were investigated under two conditions, i.e. either a low or a high correlation of linkage disequilibrium (LD) phase between the pure lines.

Results

The results demonstrate that the gain in CP was higher when parental lines were selected for CP, rather than purebred performance, both with a low and a high correlation of LD phase. For a low correlation of LD phase between the pure lines, the use of two separate reference populations yielded a higher gain in CP than use of a single reference population that combines both pure lines. However, for a high correlation of LD phase, marker effects that were estimated using a single combined reference population increased the gain in CP.

Conclusions

Under the hypothesis that performance of crossbred animals differs from that of purebred animals due to dominance, a dominance model can be used for GS of purebred individuals for CP, without using crossbred data. Furthermore, if the correlation of LD phase between pure lines is high, accuracy of selection can be increased by combining the two pure lines into a single reference population to estimate marker effects.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0099-3) contains supplementary material, which is available to authorized users.