Size Distribution of Bacterial Cells

By using differential light-scattering measurements of single cells suspended in a laser beam, an effective cell radius has been determined for 141 individual bacteria from suspensions of Staphylococcus epidermidis. The accumulation of these measurements has provided the size distribution for the sampling.     

Size of murine RNA tumor virus-specific nuclear RNA molecules.

About 1% of the total RNA of cell lines producing murine leukemia virus is virus-specific RNA. About one-third of the virus-specific RNA is located within the nucleus. The size distribution of virus-specific RNA was determined before and after denaturation. Before denaturation, virus-specific RNA sequences sedimented as a heterogeneous population of RNA molecules, some of which sedimented very rapidly. After denaturation, most of the virus-specific RNA had a sedimentation coefficient of 35S or lower, but a small fraction of the nuclear virus-specific RNA sedimented more rapidly than 35S RNA even after denaturation.     

Exponential Size Distribution of von Willebrand Factor

Von Willebrand Factor (VWF) is a multimeric protein crucial for hemostasis. Under shear flow, it acts as a mechanosensor responding with a size-dependent globule-stretch transition to increasing shear rates. Here, we quantify for the first time, to our knowledge, the size distribution of recombinant VWF and VWF-eGFP using a multilateral approach that involves quantitative gel analysis, fluorescence correlation spectroscopy, and total internal reflection fluorescence microscopy. We find an exponentially decaying size distribution of multimers for recombinant VWF as well as for VWF derived from blood samples in accordance with the notion of a step-growth polymerization process during VWF biosynthesis. The distribution is solely described by the extent of polymerization, which was found to be reduced in the case of the pathologically relevant mutant VWF-IIC. The VWF-specific protease ADAMTS13 systematically shifts the VWF size distribution toward smaller sizes. This dynamic evolution is monitored using fluorescence correlation spectroscopy and compared to a computer simulation of a random cleavage process relating ADAMTS13 concentration to the degree of VWF breakdown. Quantitative assessment of VWF size distribution in terms of an exponential might prove to be useful both as a valuable biophysical characterization and as a possible disease indicator for clinical applications.     

Egg-Mass Size and Cell Size: Effects of Temperature on Oxygen Distribution

Two processes strongly influence the distribution of oxygenwithin egg masses and cells: the supply of oxygen by diffusionand the consumption of oxygen by embryos and mitochondria. Theseprocesses are differentially sensitive to temperature. The diffusioncoefficient of oxygen depends only weakly on temperature, havinga Q₁₀ of approximately 1.4. In contrast, the consumption ofoxygen depends strongly on temperature, having a Q₁₀ between1.5 and 4.0. Thus, at higher temperatures, the ratio of oxygensupply to demand decreases. I show, by extending a model ofoxygen distribution within metabolizing spheres, that maximalegg-mass sizes and cell sizes are predicted to be smaller athigher temperatures. For egg masses, definitive data are notyet available. For ectothermic cells, this prediction appearsto be supported; cells from a variety of ectothermic organisms,unicellular and multicellular, are smaller when the cells areproduced at warmer temperatures. Establishing a specific connectionbetween this pattern and oxygen distributions requires demonstrationof (1) oxygen concentration gradients within metabolizing spheresand (2) central oxygen concentrations low enough to affect function.Egg masses from a variety of taxa show steep oxygen concentrationgradients and often are severely hypoxic or anoxic in centrallocations. Severe hypoxia appears capable of retarding developmentor killing embryos. Similar kinds of data for ectothermic cellshave not yet been collected, but the literature on oxygen gradientswithin mammalian cells suggests that intracellular gradientsmay be important.     

Exponential Size Distribution of von Willebrand Factor

Von Willebrand Factor (VWF) is a multimeric protein crucial for hemostasis. Under shear flow, it acts as a mechanosensor responding with a size-dependent globule-stretch transition to increasing shear rates. Here, we quantify for the first time, to our knowledge, the size distribution of recombinant VWF and VWF-eGFP using a multilateral approach that involves quantitative gel analysis, fluorescence correlation spectroscopy, and total internal reflection fluorescence microscopy. We find an exponentially decaying size distribution of multimers for recombinant VWF as well as for VWF derived from blood samples in accordance with the notion of a step-growth polymerization process during VWF biosynthesis. The distribution is solely described by the extent of polymerization, which was found to be reduced in the case of the pathologically relevant mutant VWF-IIC. The VWF-specific protease ADAMTS13 systematically shifts the VWF size distribution toward smaller sizes. This dynamic evolution is monitored using fluorescence correlation spectroscopy and compared to a computer simulation of a random cleavage process relating ADAMTS13 concentration to the degree of VWF breakdown. Quantitative assessment of VWF size distribution in terms of an exponential might prove to be useful both as a valuable biophysical characterization and as a possible disease indicator for clinical applications.     

Size differences of large ribosomal RNA in vertebrates

By using a modification of acrylamide gel electrophoresis in the presence of 95 per cent formamide it is shown that real differences exist in the size of rRNA of the large ribosomal subunit (LrRNA) in vertebrates. Comparative studies on fractionation of LrRNA's in unfolded state (polyacrylamide-formamide gel) and when the conformation of RNA is preserved (agar gel) revealed that LrRNA from different classes of vertebrates show different conformations.     

RNA Control of HIV-1 Particle Size Polydispersity

HIV-1, an enveloped RNA virus, produces viral particles that are known to be much more heterogeneous in size than is typical of non-enveloped viruses. We present here a novel strategy to study HIV-1 Viral Like Particles (VLP) assembly by measuring the size distribution of these purified VLPs and subsequent viral cores thanks to Atomic Force Microscopy imaging and statistical analysis. This strategy allowed us to identify whether the presence of viral RNA acts as a modulator for VLPs and cores size heterogeneity in a large population of particles. These results are analyzed in the light of a recently proposed statistical physics model for the self-assembly process. In particular, our results reveal that the modulation of size distribution by the presence of viral RNA is qualitatively reproduced, suggesting therefore an entropic origin for the modulation of RNA uptake by the nascent VLP.     

Informational content of mitochondrial DNA from a "low density" petite mutant of yeast

Mitochondrial DNA from wild-type yeast $\text{Saccharomyces cerevisiae}$ contains the genetic information for some mitochondrial tRNAs including tRNA_ser and tRNA_phe. In a “low density” petite mutant, mitochondrial DNA still retains the information for tRNA_ser, while the information for tRNA_phe is lost.The permanence of genetic information in this DNA containing only 3.6% G+C supports previous results concerning its intramolecular heterogeneity. An irregular distribution of G+C content along the molecule was further demonstrated by annealing experiments performed with DNA fragmented by sonication and fractionated on CsCl density gradient. These experiments show that the heavy fractions of the gradient preferentially anneal with mitochondrial seryl-tRNA.     

Simulating Stationary Size Distribution of Trees in Rain Forests

A simple dynamic model of the distribution of tree size (trunkdiameter) in natural rain forests is presented. Based on dataof permanent plot measurements in a tropical rain forest anda warm-temperate rain forest, the cumulative basal area densityof trees larger than a given tree, at any particular time, isused to express the effect of suppression, or one-sided competition,on the growth rate of that tree. It also shows that increasingthe basal area density of all trees in the stand depresses therate of recruitment from the pool of seedlings. Mortality istreated as independent of the cumulative basal area. Simulationwith the model, applying the one-dimensional drift-diffusionequation, reproduces the observed course of reforestation afterclear-felling and leads to convergence to a unique stationarysize distribution by 200 years. This concuts with the size distributionobserved in primary forest stands. The present model representsan extension of density-dependent population growth models tosize-structured tree populations. Competition, cumulative basal area, density dependence, equilibrium, population, simulation, size distribution, tropical rain forest, warm—temperate rain forest     

Uneven Distribution and Size of Rabbit Lens Capsule Proteoglycans

To document the ultrastructural distribution of lens capsule proteoglycans, rabbit lens capsules were fixed and stained overnight in 50mM sodium acetate, pH 5.6, containing 2.5% glutaraldehyde, 0.2% Cuprolinic Blue and 0.2M MgCl2. They were rinsed, stained with 1% aqueous sodium tungstate, embedded in Epon, sectioned (60nm), and examined with an electron microscope at 60kV.Proteoglycan–Cuprolinic Blue complexes mainly appeared as networks of small electron-dense filaments throughout the posterior and anterior capsules. The posterior capsule was a single layer with a network of small proteoglycan filaments gradually decreasing in size from the humoral side (90×10nm) to the lenticular side (30×8nm). The humoral side of the anterior capsule had a thin lamina (400nm) containing large (180×40nm), very electron-dense proteoglycan–Cuprolinic Blue complexes plus small proteoglycans. Below this lamina, the complexes were only seen as filaments slightly smaller than those in the corresponding area of the posterior capsule.Cuprolinic Blue binding of the anterior and posterior lens capsules revealed differences in the size and distribution of their sulphated proteoglycans which do not correspond to the patterns of their immunoreactivity with anti-heparan sulphate proteoglycan. The humoral lamina in the anterior capsules, with large proteoglycan structures, might be a distinct structural and functional compartment.     

Size selective recognition of siRNA by an RNA silencing suppressor

RNA silencing in plants likely exists as a defense mechanism against molecular parasites such as RNA viruses, retrotransposons, and transgenes. As a result, many plant viruses have adapted mechanisms to evade and suppress gene silencing. Tombusviruses express a 19 kDa protein (p19), which has been shown to suppress RNA silencing in vivo and bind silencing-generated and synthetic small interfering RNAs (siRNAs) in vitro. Here we report the 2.5 A crystal structure of p19 from the Carnation Italian ringspot virus (CIRV) bound to a 21 nt siRNA and demonstrate in biochemical and in vivo assays that CIRV p19 protein acts as a molecular caliper to specifically select siRNAs based on the length of the duplex region of the RNA.     

Size heterogeneity of polyadenylate sequences in mouse globin messenger RNA

Heterogeneity in the length of the poly(A) region has been demonstrated in mouse α and β-globin messenger RNAs. This finding is based on the initial observation that only 30% of the globin mRNA purified by oligo(dT)-cellulose affinity chromatography binds to Millipore filters under conditions where other poly(A)-containing mRNAs have been shown to bind, and the subsequent finding that the bound and non-bound fractions contain different size classes of poly(A). The poly(A) size was determined by polyacrylamide gel electrophoresis of the T₁ and pancreatic RNAase-resistant fragments. The unbound mRNA fraction gives a fragment 35 to 45 adenine nucleotides long, while the bound mRNA contains two fragments with average lengths of 55 to 65 and 75 to 120 nucleotides.The heterogeneity of the poly(A) region is present in both α and β-globin mRNAs as both Millipore-bound and unbound RNA fractions directed the synthesis of comparable amounts of mouse α and β-globin chains.Change in the distribution of the various size classes of poly(A) was analyzed by Millipore binding assays after various times of labeling in vivo. The percentage of labeled mRNA bound to Millipore filters decreased with time, suggesting either a shortening of the poly(A) region or differential synthesis of mRNAs containing shorter poly(A) at earlier stages in erythropoeisis.     

Special Issue on "RNA Epigenetics"

正We are very pleased to announce a special issue,to be published in April 2017,on‘‘RNA Epigenetics’’in the journal Genomics,ProteomicsBioinformatics(GPB).RNAs are life’s essential molecules with diverse functions.The identification and functional studies of multiple types of non-coding RNAs have been a major focus of life science research during the past decade.Moreover,diversified chemical modifications as well as structural     

Industrial Production and Quality Control of Two Liposome Gels: Size,Size Distribution and Stability

Abstract

We use the mechanical high-shear homogenization method for large scale production of two cosmetic gels containing a liposome dispersion. To ensure homogeneity, reproducibility and stability, transmission electron-microscope techniques were used to determine particle size and size distribution of vesicles, in addition to other techniques such as flow cytometry fluorescence and Coulter analysis.     

Particle Size Distribution Equivalency as Novel Predictors for Bioequivalence

The use of particle size distribution (PSD) similarity metrics and the development and incorporation of drug release predictions based on PSD properties into PBPK models for various drug administration routes may provide a holistic approach for evaluating the effect of PSD differences on in vitro drug release and bioavailability of disperse systems. The objectives of this study were to provide a rational approach for evaluating the utility of in vitro PSD comparators for predicting bioequivalence for subcutaneously administered test and reference drug emulsions. Two types of in vitro comparators for test and reference emulsion products were evaluated: PSD characterization comparators (overlap metrics, median, and span ratios) and release profile comparators (f₂ and various fractional time ratios). A subcutaneous-input PBPK disposition model was developed to simulate blood concentration-time profiles of reference and test emulsion products and pharmacokinetic responses (e.g., AUC, C_max, and T_max) were used to determine bioequivalence. A pool of 10,440 pairs of test and reference products was simulated using Monte Carlo experiments. The PSD and release profile comparators were correlated to pass/fail bioequivalence metrics using logistical regression. Based on the use of single in vitro comparators, the f₂ method was the best predictor of bioequivalence prediction. The use of combinations of f₂ and PSD overlap comparators (e.g., OVL or PROB) improved bioequivalence prediction to about 90%. Simulation procedures used in this study demonstrated a process for developing reliable in vitro BE predictors.