Synchronization of Escherichia coli by Zonal Centrifugation

A zonal centrifugation technique that can select the smallest newborn cells in an exponentially growing culture of Escherichia coli B/r is described.     

Differential RNA Metabolism in Rat Brain Cells Fractionated by Zonal Centrifugation

Combined fractionation and RNA metabolism studies were made on homologous cell types (neurons and glia) banded from rat brain cerebral cortex and hippocampus tissue at 40, 000 rev/min for 50 minutes in a Beckman Ti 14 zonal rotor loaded with a discontinuous methyl cellulose (Methocel) and sucrose density gradient. Comparisons were made on the cellular fractions recovered from animals intracisternally injected with 15 μCi tritiated cytidine (³HCR) RNA precursor one hour before sacrifice and tissue cellular filtrate preparation. Immediate³H pool-correction of extracted³HRNA from the three cellular Bands recovered made possible a mathematically valid measure of³HCR-precursor incorporation into RNA of the different cell types. Comparison of the cellular³HRNA data by analysis of variance revealed the occurrence of differential tritium labelling of RNA in the same cell types banded from different brain regions. In particular, an important advance was demonstrated by the procedures developed in these studies for the quantitative cellular assay of brain in vivo (differential) RNA metabolism.     

Isolation of Intact Chloroplasts from Euglena gracilis by Zonal Centrifugation

Chloroplasts were separated from Euglena gracilis by zonal centrifugation at low speed in density gradients of Ficoll or dextran. The chloroplasts were intact by the criteria of ultrastructure and their content of ribulose diphosphate carboxylase and soluble protein. The chloroplasts also contained ribosomes and ribosomal RNA uncontaminated by the corresponding cytoplasmic particles.     

Separation of Treponema pallidum from Tissue Substances by Continuous-Flow Zonal Centrifugation

The zonal ultracentrifuge was used for separation of Treponema pallidum from large volumes of rabbit testicular syphiloma extracts by continuous-flow centrifugation in a cesium chloride density gradient. The gradient was linear with radius from a density of 1.05 to 1.36 g/ml. Operating speeds were 15,000 rev/min for the continuous-flow phase and 25,000 rev/min for a 30-min banding period. A total of 9 x 10(9) (24.3%) treponemes were recovered from the original extract. Of the treponemes recovered, 88% formed a band at a density of 1.170 to 1.211 g/ml. Within the limits of present methods of assay, these fractions were relatively free from testicular particulates and protein when compared with treponemes recovered after differential centrifugation. Observations of the isolated fractions by dark-field and electron microscopy indicated a lack of gross morphological damage to T. pallidum. Their antigenic characteristics were also retained, as evidenced by their ability to react with syphilitic sera in the indirect fluorescent-antibody procedure.     

Use of Yeast Populations Fractionated by Zonal Centrifugation to Study the Cell Cycle

Zonal centrifugation in a sucrose density gradient was used to separate yeast cells primarily by size and thus by age in the cell cycle. This approach provides an alternative to synchronous growth for examining the properties of cells at different stages in the cell cycle.     

Purification of Large Quantities of Coxiella burnetii Rickettsia by Density Gradient Zonal Centrifugation

The purification of large quantities of inactivated, phase II Coxiella burnetii by isopycnic zonal centrifugation for use as diagnostic antigen and as a vaccine is described. The fractionation of egg yolk sac-derived C. burnetii vaccine resulted in the separation of two distinct populations of organisms, each devoid of microscopically and serologically recognizable components of egg yolk sac. One population of organisms, characterized by an equilibrium density of 1.240, was rod shaped (1.0 by 0.5 μmole) with a thick, densely strained wall and prominent central body. The second population, with an equilibrium density of 1.280, had a coccobacillary shape (approximately 1 μmole in diameter), granular, sometimes fibrillar cytoplasm, thin cellular walls, and lacked a prominent nucleoid.     

大规模区带离心纯化Vero细胞乙脑疫苗

本文报道一种适合疫苗生产的大规模纯化Ｖｅｒｏ细胞乙脑疫苗的方法。原疫苗经适当浓缩和去除ＤＮＡ处理后,用不连续蔗糖梯度（３６％和６０％）。３２６００ｇ,速率区带离心４ｈ。纯化后疫苗的效力比中国参考疫苗高出６倍以上,补体结合抗原比中国参考疫苗高４～８倍。总蛋白含量低于３０μｇ／ｍＬ,牛血清含量降至０．５μｇ／ｍＬ以下,细胞残余ＤＮＡ低于１００ｐｇ／０．５ｍＬ。用此法连续制备三批纯化疫苗,其纯度和效力均高于日本鼠脑纯化疫苗。此法对于制备其它纯化Ｖｅｒｏ细胞疫苗也具有一定的参考意义。     

Fractionation of Isolated Rat CNS Myelinated Axons by Sucrose Density Gradient Centrifugation in a Zonal Rotor

Myelinated axons isolated from rat CNS brain stem by flotation in a buffered sucrose-salt medium were shocked by vigorous homogenization in hypotonie buffer and then fractionated on a 20-40% (wt/wt) linear sucrose gradient in a Beckman Ti-14 Zonal Rotor. After centrifu-gation to equilibrium, the gradient was fractionated on the basis of sucrose density into 13 individual fractions. The distributions of molecular markers related to myelin [(myelin basic protein, 2’3′-cyclic nucleotide 3′-phos-phodiesterase (EC 3.1.4.37), myelin-associated glycopro-tein (MAG)]; microsomes [CDP-choline:l,2 diglyceride cholinephosphotransferase (EC 2.7.8.2)]; mitochondria [cytochrome c oxidase (EC 1.9.3.1), monoamine oxidase (amine:oxygen oxidoreductase, deaminating, EC 1.4.3.4)], and axolemma [acetylcholinesterase (acetylcho-line hydrolase, EC 3.1.1.7), 5′-nucleotidase (5′-ribonu-cleotide phosphohydrolase, EC 3.1.3.5), Na⁺,K⁺-adeno-sine triphosphatase (EC 3.6.1.3), [³H]saxitoxin binding] were examined, as well as the protein composition and morphological appearance of the fractions. The myelin-related markers were most enriched in the 20-26% region of the gradient, although the MAG was broadly distributed throughout the entire gradient. The axolemma-related markers were most enriched in the 28-32% region of the gradient, whereas the microsomal and mitochondrial-related markers were enriched in the 35-40% region of the sucrose density gradient. Mixing experiments utilizing ¹²⁵I-labeled membrane preparations derived from cultured oligodendroglial and astroglial cells indicated that the constituents of the shocked myelinated axons were not significantly contaminated with glial membranes. The morphology of the fraction was consistent with the membrane molecular marker distribution: the light end of the gradient contained multilamellar myelin; fractions in the center of the gradient were enriched in un-ilamellar membrane fragments; the densest regions of the gradient were enriched in mitochondria. The myelin specific proteins were the prominent polypeptides in the 20-25% regions of the gradient, whereas polypeptides having a molecular weight of 50,000 or greater predominanted in the denser regions of the gradient. The significance of the distribution of these membrane markers and the utility of this fractionation procedure are discussed.     

Large-Scale Purification of Ribonucleic Acid Tumor Viruses by Use of Continuous-Flow Density Gradient Centrifugation

This report describes a 200- to 300-fold increase in the quantity of ribonucleic acud tumor virus particles previously isolated at one time by zonal centrifugation.     

Integrated Assessment of Large-Scale Biofuel Production

This paper proposes a different framework for discussing the possibility of replacing a significant fraction of fossil energy consumption of modern economies with biofuels. The proposed analysis is not based on the two classic feasibility checks—land availability and output/input energy ratio—debated in the majority of the literature in this field. Rather, the focus is on the desirability of an energy sector powered by biomass energy. Discussing of desirability requires introducing a multicriteria approach, that in turn requires a definition of a set of criteria of performance for such an energy sector. The concepts of societal metabolism and ecosystem metabolism are introduced to define five criteria of performance for an energy sector powered by alternative sources.

This paper does not tell the society whether or not biofuels should be used to replace fossil energy. Rather, it proposes a method of characterization of pros and cons for the option biofuel which can be used to make more informed choices. An analysis of three systems of production—corn-ethanol, sunflower-biodiesel, and SRWC-methanol—is provided to indicate the existence of systemic characteristics associated with an energy sector powered by biofuels. These characteristics are likely to persist even when different technical coefficients will be achieved. The conclusion is that, at the moment, it is not possible to replace the actual performance of an energy sector based on fossil energy with an energy sector running on biofuel. Biomass energy can and will have to play an important role in the sustainability of humankind, but this will require a better understanding of (i) the role that an energy sector plays within a given structure of societal metabolism; and (ii) the impact generated on ecosystem metabolism by societal metabolism, plus a lot of wisdom.     

Alzheimer's Disease Risk Assessment Using Large-Scale Machine Learning Methods

The goal of this work is to introduce new metrics to assess risk of Alzheimer''s disease (AD) which we call AD Pattern Similarity (AD-PS) scores. These metrics are the conditional probabilities modeled by large-scale regularized logistic regression. The AD-PS scores derived from structural MRI and cognitive test data were tested across different situations using data from the Alzheimer''s Disease Neuroimaging Initiative (ADNI) study. The scores were computed across groups of participants stratified by cognitive status, age and functional status. Cox proportional hazards regression was used to evaluate associations with the distribution of conversion times from mild cognitive impairment to AD. The performances of classifiers developed using data from different types of brain tissue were systematically characterized across cognitive status groups. We also explored the performance of anatomical and cognitive-anatomical composite scores generated by combining the outputs of classifiers developed using different types of data. In addition, we provide the AD-PS scores performance relative to other metrics used in the field including the Spatial Pattern of Abnormalities for Recognition of Early AD (SPARE-AD) index and total hippocampal volume for the variables examined.     

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to explore the binding mechanisms. Several strategies have been proposed, but the state-of-the-art approaches display a great diversity in i) the definition of nucleic acid binding sites; ii) the training and test datasets; iii) the algorithmic methods for the prediction strategies; iv) the performance measures and v) the distribution and availability of the prediction programs. Here we report a large-scale assessment of 19 web servers and 3 stand-alone programs on 41 datasets including more than 5000 proteins derived from 3D structures of protein-nucleic acid complexes. Well-defined binary assessment criteria (specificity, sensitivity, precision, accuracy…) are applied. We found that i) the tools have been greatly improved over the years; ii) some of the approaches suffer from theoretical defects and there is still room for sorting out the essential mechanisms of binding; iii) RNA binding and DNA binding appear to follow similar driving forces and iv) dataset bias may exist in some methods.     

Large-Scale Assessment of Mediterranean Marine Protected Areas Effects on Fish Assemblages

Marine protected areas (MPAs) were acknowledged globally as effective tools to mitigate the threats to oceans caused by fishing. Several studies assessed the effectiveness of individual MPAs in protecting fish assemblages, but regional assessments of multiple MPAs are scarce. Moreover, empirical evidence on the role of MPAs in contrasting the propagation of non-indigenous-species (NIS) and thermophilic species (ThS) is missing. We simultaneously investigated here the role of MPAs in reversing the effects of overfishing and in limiting the spread of NIS and ThS. The Mediterranean Sea was selected as study area as it is a region where 1) MPAs are numerous, 2) fishing has affected species and ecosystems, and 3) the arrival of NIS and the northward expansion of ThS took place. Fish surveys were done in well-enforced no-take MPAs (HP), partially-protected MPAs (IP) and fished areas (F) at 30 locations across the Mediterranean. Significantly higher fish biomass was found in HP compared to IP MPAs and F. Along a recovery trajectory from F to HP MPAs, IP were similar to F, showing that just well enforced MPAs triggers an effective recovery. Within HP MPAs, trophic structure of fish assemblages resembled a top-heavy biomass pyramid. Although the functional structure of fish assemblages was consistent among HP MPAs, species driving the recovery in HP MPAs differed among locations: this suggests that the recovery trajectories in HP MPAs are likely to be functionally similar (i.e., represented by predictable changes in trophic groups, especially fish predators), but the specific composition of the resulting assemblages may depend on local conditions. Our study did not show any effect of MPAs on NIS and ThS. These results may help provide more robust expectations, at proper regional scale, about the effects of new MPAs that may be established in the Mediterranean Sea and other ecoregions worldwide.     

Zonal unit-gravity elutriation

A new and simple technique, zonal unit-gravity elutriation, has been devised for separating very large cells, multicellular complexes, or small organisms from suspensions consisting mainly of small cells. The separation vessel is a conical chamber with an entrance at the lower, narrower part of the cone and an exit at the upper, wider part of the cone via a dome-shaped lid. A baffle at the entrance prevents turbulence from incoming fluid. Chambers of differing widths and wall slopes are chosen depending on the sedimentation rate of the particles to be separated. A small volume of the cell suspension is placed in the chamber on the bench in a cold-room. Medium stabilized by a shallow density gradient is pumped into the base of the chamber and ascends, creating a decreasing velocity gradient. Cells sediment at unit-gravity against this ascending counterstream, and are separated into bands according to sedimentation velocity. By adjusting the flow rate of the medium, different sizes of cells can be separated. Tumor cells can be enriched, and larger blast cells can be separated from small cells in lymphoid cell suspensions. The procedure produces complete separation of thymic nurse cells (epithelial-lymphoid complexes) from free thymocytes in digested thymus suspensions and produces substantial enrichment of thymic rosettes (macrophage-lymphoid complexes). A very favorable situation for applying this technique is the isolation ofTaenia taeniaformis larvae, which can be completely purified from infected liver suspensions, representing a 4×10⁵-fold enrichment of the parasites, with high recovery, in a single 30 min operation.     

Centrifugation or filtration in quantitative radioreceptor assays

In quantitative radioreceptor assays the amount of a drug present in the medium to be assayed is inversely related to the amount of receptor-bound radiolabelled ligand. Usually, separation of the bound and free fractions of radiolabelled ligand is done by filtration, in which the bound fraction can easily be collected. However, the filtration disturbs the equilibrium between bound and free fractions, which may lead to erroneous results. Because the decrease in bound radiolabelled ligand is accompanied by an increase in free labelled ligand, we decided also to measure this free fraction after separation by centrifugation and to compare these data with the filtration data. In these experiments a radioreceptor assay for anticholinergics was employed. The results indicate that both methods are compatible in precision when appropriate conditions are used whereas each method has its specific features.     

In-vivo Centrifugation of Drosophila Embryos

A major strategy for purifying and isolating different types of intracellular organelles is to separate them from each other based on differences in buoyant density. However, when cells are disrupted prior to centrifugation, proteins and organelles in this non-native environment often inappropriately stick to each other. Here we describe a method to separate organelles by density in intact, living Drosophila embryos. Early embryos before cellularization are harvested from population cages, and their outer egg shells are removed by treatment with 50% bleach. Embryos are then transferred to a small agar plate and inserted, posterior end first, into small vertical holes in the agar. The plates containing embedded embryos are centrifuged for 30 min at 3000g. The agar supports the embryos and keeps them in a defined orientation. Afterwards, the embryos are dug out of the agar with a blunt needle.Centrifugation separates major organelles into distinct layers, a stratification easily visible by bright-field microscopy. A number of fluorescent markers are available to confirm successful stratification in living embryos. Proteins associated with certain organelles will be enriched in a particular layer, demonstrating colocalization. Individual layers can be recovered for biochemical analysis or transplantation into donor eggs. This technique is applicable for organelle separation in other large cells, including the eggs and oocytes of diverse species.     

Large-Scale Assessment of the Effect of Popularity on the Reliability of Research

Based on theoretical reasoning it has been suggested that the reliability of findings published in the scientific literature decreases with the popularity of a research field. Here we provide empirical support for this prediction. We evaluate published statements on protein interactions with data from high-throughput experiments. We find evidence for two distinctive effects. First, with increasing popularity of the interaction partners, individual statements in the literature become more erroneous. Second, the overall evidence on an interaction becomes increasingly distorted by multiple independent testing. We therefore argue that for increasing the reliability of research it is essential to assess the negative effects of popularity and develop approaches to diminish these effects.     

Large-Scale Assessment of a Fully Automatic Co-Adaptive Motor Imagery-Based Brain Computer Interface

In the last years Brain Computer Interface (BCI) technology has benefited from the development of sophisticated machine leaning methods that let the user operate the BCI after a few trials of calibration. One remarkable example is the recent development of co-adaptive techniques that proved to extend the use of BCIs also to people not able to achieve successful control with the standard BCI procedure. Especially for BCIs based on the modulation of the Sensorimotor Rhythm (SMR) these improvements are essential, since a not negligible percentage of users is unable to operate SMR-BCIs efficiently. In this study we evaluated for the first time a fully automatic co-adaptive BCI system on a large scale. A pool of 168 participants naive to BCIs operated the co-adaptive SMR-BCI in one single session. Different psychological interventions were performed prior the BCI session in order to investigate how motor coordination training and relaxation could influence BCI performance. A neurophysiological indicator based on the Power Spectral Density (PSD) was extracted by the recording of few minutes of resting state brain activity and tested as predictor of BCI performances. Results show that high accuracies in operating the BCI could be reached by the majority of the participants before the end of the session. BCI performances could be significantly predicted by the neurophysiological indicator, consolidating the validity of the model previously developed. Anyway, we still found about 22% of users with performance significantly lower than the threshold of efficient BCI control at the end of the session. Being the inter-subject variability still the major problem of BCI technology, we pointed out crucial issues for those who did not achieve sufficient control. Finally, we propose valid developments to move a step forward to the applicability of the promising co-adaptive methods.