Changes in DNA superhelical density monitored by polarized light scattering.

Linear and circular lambda-DNA at different ethidium bromide concentrations have been studied by means of polarized light scattering, namely the S14, S34, S33 and S13 elements of Mueller matrix. While S33 at low angle appears well correlated with the total light scattering evaluated by optical density measurements at 632.8 nm for linear and circular DNA of the same mass, the magnitude and slope of the S14, S34 and S13 signals display significant changes for the circular lambda-DNA depending on the degree of negative superhelical density as induced by the different ethidium bromide concentrations. At the same time, for linear lambda-DNA the signal remains invariant, making explicit for the differential scattering of polarized light the possibility to obtain additional information by its angular dependence. Strikingly also the effect of 0.2% glutaraldehyde versus ethanol fixation on the native lambda-DNA structural properties appears to confirm earlier findings by other well-established probes. Results are discussed in terms of first physical principles and of their potential bearings towards our understanding of the mechanism controlling gene expression.     

Measuring diameters of rod-shaped bacteria in vivo with polarized light scattering.

The angular function for elements of the Mueller matrix for polarized light scattering from suspensions of microorganisms is known to be reproducible for different growths of a given bacterial strain in the log (or exponential) phase of growth. The reason for this, the stability of the size and shape distribution for cells, is briefly discussed. Experiments were performed using suspensions of two different strains of Escherichia coli cells in log phase and measuring the angular dependence of the Mueller matrix ratio S34/S11. Calculations were then performed using the coupled dipole approximation to model electromagnetic scattering from particles where the shape of an individual cell was approximated by a cylinder capped with hemispheres of the same radius as the cylinder. Using previously measured values for the length distribution and index of refraction of the cells, the calculated scattering curve was found to fit the measured curve very well. The values obtained for the cell diameters were quite close to diameters previously measured by optical microscopy. Thus this method provides a rapid and convenient method for monitoring bacterial diameters in vivo even when there is an appreciable distribution of bacterial lengths in the population.     

Polarized light scattering for rapid observation of bacterial size changes.

The effect of changing growth conditions on the diameter of rod-shaped bacteria was studied in vivo with the use of polarized light scattering. The value of a ratio of scattering matrix elements was measured as a function of scattering angle at various times after nutritional "upshift" for two strains of Escherichia coli cells. The peak locations of the scattering function were calibrated against the diameter for rod-shaped bacteria. The peaks moved toward smaller angles as a function of time after upshift, indicating that the diameter was increasing. Under special conditions, substantial peak shifts occurred within a few minutes of growth condition change, indicating a rapid onset of growth in diameter. The rate of increase of the diameters after upshift was obtained from the angular shift of peak location. This rate was approximately 14 nm/min for E. coli K12 and approximately 9 nm/min for E. coli B/r at 37 degrees C. The rate of diameter increase is smaller at lower temperatures. Experiments with Bacillus megaterium showed that any diameter change after nutritional upshift at 37 degrees C is limited to at most a very small increase, at least for the strain and medium tested.     

Mueller matrix decomposition for polarized light assessment of biological tissues

The Mueller matrix represents the transfer function of an optical system in its interactions with polarized light and its elements relate to specific biologically or clinically relevant properties. However, when many optical polarization effects occur simultaneously, the resulting matrix elements represent several “lumped” effects, thus hindering their unique interpretation. Currently, no methods exist to extract these individual properties in turbid media. Here, we present a novel application of a Mueller matrix decomposition methodology that achieves this objective. The methodology is validated theoretically via a novel polarized‐light propagation model, and experimentally in tissue simulating phantoms. The potential of the approach is explored for two specific biomedical applications: monitoring of changes in myocardial tissues following regenerative stem cell therapy, through birefringence‐induced retardation of the light's linear and circular polarizations, and non‐invasive blood glucose measurements through chirality‐induced rotation of the light's linear polarization. Results demonstrate potential for both applications. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Polarized diffuse reflectance measurements on cancerous and noncancerous tissues

We report the measurement of polarization parameters (linear retardance, diattenuation and depolarization) of normal and malignant tissue from human oral cavity and breast over the spectral range 390 nm to 550 nm. These parameters were determined using the 3 × 3 Mueller matrix, the elements of which could be determined using linear polarization measurements only. The significant differences observed in the polarization parameters of the normal and malignant tissues appear to arise because of the changes in the collagen matrix in the two tissue types. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Conformation of reconstituted mononucleosomes and effect of linker histone H1 binding studied by scanning force microscopy

The conformation of mononucleosome complexes reconstituted with recombinant core histones on a 614-basepair-long DNA fragment containing the Xenopus borealis 5S rRNA nucleosome positioning sequence was studied by scanning/atomic force microscopy in the absence or presence of linker histone H1. Imaging without prior fixation was conducted with air-dried samples and with mononucleosomes that were injected directly into the scanning force microscopy fluid cell and visualized in buffer. From a quantitative analysis of approximately 1,700 complexes, the following results were obtained: i), In the absence of H1, a preferred location of the nucleosome at the X. borealis 5S rRNA sequence in the center of the DNA was detected. From the distribution of nucleosome positions, an energy difference of binding to the 5S rRNA sequence of DeltaDeltaG approximately 3 kcal mol(-1) as compared to a random sequence was estimated. Upon addition of H1, a significantly reduced preference of nucleosome binding to this sequence was observed. ii), The measured entry-exit angles of the DNA at the nucleosome in the absence of H1 showed two maxima at 81 +/- 29 degrees and 136 +/- 18 degrees (air-dried samples), and 78 +/- 25 degrees and 137 +/- 25 degrees (samples imaged in buffer solution). In the presence of H1, the species with the smaller entry-exit angle was stabilized, yielding average values of 88 +/- 34 degrees for complexes in air and 85 +/- 10 degrees in buffer solution. iii), The apparent contour length of the nucleosome complexes was shortened by 34 +/- 13 nm as compared to the free DNA due to wrapping of the DNA around the histone octamer complex. Considering an 11 nm diameter of the nucleosome core complex, this corresponds to a total of 145 +/- 34 basepairs that are wound around the nucleosome.     

Imaging linear and circular polarization features in leaves with complete Mueller matrix polarimetry

Spectropolarimetry of intact plant leaves allows to probe the molecular architecture of vegetation photosynthesis in a non-invasive and non-destructive way and, as such, can offer a wealth of physiological information. In addition to the molecular signals due to the photosynthetic machinery, the cell structure and its arrangement within a leaf can create and modify polarization signals. Using Mueller matrix polarimetry with rotating retarder modulation, we have visualized spatial variations in polarization in transmission around the chlorophyll a absorbance band from 650?nm to 710?nm. We show linear and circular polarization measurements of maple leaves and cultivated maize leaves and discuss the corresponding Mueller matrices and the Mueller matrix decompositions, which show distinct features in diattenuation, polarizance, retardance and depolarization. Importantly, while normal leaf tissue shows a typical split signal with both a negative and a positive peak in the induced fractional circular polarization and circular dichroism, the signals close to the veins only display a negative band. The results are similar to the negative band as reported earlier for single macrodomains. We discuss the possible role of the chloroplast orientation around the veins as a cause of this phenomenon. Systematic artefacts are ruled out as three independent measurements by different instruments gave similar results. These results provide better insight into circular polarization measurements on whole leaves and options for vegetation remote sensing using circular polarization.     

Changes in the Composition and Size Distribution of Soymilk Protein Particles by Heating

The protein particles in soymilk were fractionated in size by differential centrifugation. Particles of more than 100 nm in diameter (LSP) constituted 40% of the total protein in raw soymilk, 70% of the protein components being 11S globulin. LSP was not formed in the presence of 2-mercaptoethanol and sodium ascorbate. LSP was decreased by heating, and particles of 100–40 nm in diameter (MSP) were increased. The formation of MSP was not due to any degradation of LSP but to the combination of supernatant proteins of less than 40 nm in diameter with each other. MSP formed by heating contained the β subunit of 7S and the basic subunit of 11S as main components. The particles of more than 40 nm in diameter (LSP + MSP) constituted 50% of the total protein in both raw soymilk and soymilk.     

Changes in cell diameter during the division cycle of Escherichia coli

Extensive measurements of steady-state populations of several Escherichia coli strains have consistently indicated that cell diameter decreases with increasing cell length. This was observed both after electron microscopy of air-dried cells and after phase-contrast microscopy of living cells. The analysis was made by considering separately the unconstricted cells and three classes (slight, medium, and deep) of constricted cells in the population. During slow growth, cells with the average newborn length were up to 8% thicker than unconstricted cells twice as long. This decrease in diameter is less at higher growth rates. Despite the small changes and the large variation of the diameter in any particular length class, significant negative correlations between diameter and length were obtained. Cell diameter increases again at the end of the cell cycle as indicated by an increase of average diameter in the three consecutive classes of constriction.     

Morphological variation of immunoreactive cells positive to cholecystokinin 33 (10–20) and gastrin 34 (1–15) in human duodenum

Summary Human duodenal endocrine cells reactive with antibodies to cholecystokinin (CCK) 33 (10–20) and/or gastrin 34 (1–15) were studied by a combination of immunohistochemical and electron-microscopic methods. By immunohistochemistry, three types of endocrine cells were distinguished in human duodenal mucosa, i.e., those only positive for only CCK, those positive for both CCK and gastrin and those only positive for only gastrin. Ultrastructurally, the first cell type is characterized by many secretory granules with an eccentric dense core (mean diameter; 271+-74 nm). The second cell type, which was less frequent than the other two, has ultrastructural features that resemble type-I cells. The last cell type was composed of two types of cells containing small secretory granules identical to those of IG cells (mean diameter; 171+-31 nm) or large secretory granules indistinguishable from those of I cells (mean diameter; 286+-50 nm).     

Relative growth and morphological sexual maturity of the freshwater crab Trichodactylus fluviatilis Latreille 1828 (Decapoda,Trichodactylidae) from west central São Paulo State,Brazil

An analysis of relative growth was performed to determine the size at morphological sexual maturity of Trichodactylus fluviatilis Latreille 1828. Samples were collected by trapping at night from January 2010 through June 2011 from the Barreiro River (22°34′42″S; 49°11′92″W), west central São Paulo State, Brazil. The following measurements were obtained (mm): carapace width (CW) (independent variable), cheliped propodus length (PL), cheliped propodus height (PH), cheliped propodus width (PW), first pleopod length, and abdomen width (AW). The males showed positive allometry in the juvenile and adult stages for the following relationships: PL vs. CW, PH vs. CW, and PW vs. CW. In the females, a positive allometry was observed for AW vs. CW in the juvenile stage, and a negative allometry was observed for this relationship in the adult stage. The differential growth of the chelipeds in males could be related to territorial conflict and courtship, whereas the changes in the growth of the female abdomen most likely favor higher reproductive success.     

Optimizing the classification of biological tissues using machine learning models based on polarized data

Polarimetric data is nowadays used to build recognition models for the characterization of organic tissues or the early detection of some diseases. Different Mueller matrix-derived polarimetric observables, which allow a physical interpretation of a specific characteristic of samples, are proposed in literature to feed the required recognition algorithms. However, they are obtained through mathematical transformations of the Mueller matrix and this process may loss relevant sample information in search of physical interpretation. In this work, we present a thorough comparative between 12 classification models based on different polarimetric datasets to find the ideal polarimetric framework to construct tissues classification models. The study is conducted on the experimental Mueller matrices images measured on different tissues: muscle, tendon, myotendinous junction and bone; from a collection of 165 ex-vivo chicken thighs. Three polarimetric datasets are analyzed: (A) a selection of most representative metrics presented in literature; (B) Mueller matrix elements; and (C) the combination of (A) and (B) sets. Results highlight the importance of using raw Mueller matrix elements for the design of classification models.     

Electron microscopy of virulent phages for Streptococcus lactis.

Electron microscopic studies were made on eight virulent Streptococcus lactis bacteriophages. These phages were taken as representative of eight host range groups established in a study of 75 phage isolates and 253 hosts (213 S. lactis, 22 S. cremoris, 18 S. diacetilactis). The phages studied were shown to have an isometric hexagonal head and noncontractile tails, usually several times longer than the head diameter. The virus heads were octahedral. The phages investigated represented three morphological types on the basis of head diameter , tail thickness, and tail length. These dimensions were approximately: for type I phages, 63, 172, and 11 nm, respectively; type II, 73, 200, and 20 nm, respectively; and type III, represented here by a single phage, 98, 551, and 12 nm, respectively. The tail surface revealed a different arrangment of the structural subunits which lent a helical appearance to the tails of type I and II phages and a guaffered tube appearance to the tail of type III phage. The number of turns along the tail axis, turn length, axial pitch, and helix angle were: type I, 32, 12 to 13 nm, 7.14 nm, and 11 degrees 43', respectively; type II, 24, 24, to 28 nm, 40.00 nm, and 32 degrees 30', respectively; and type III, 120, 12 nm, and no visible slope towards the axis. The morphology types showed complete correlation with serological groups, but not with groups based on host range pattern.     

Ultrastructure of the Bacteroides nodosus cell envelope layers and surface.

The surface structure and cell envelope layers of various virulent Bacteroides nodosus strains were examined by light microscopy and by electron microscopy by using negative staining, thin-section, and freeze-fracture-etch techniques. Three surface structures were described: pili and a diffuse material, both of which emerged from one or both poles of the bacteria (depending on the stage of growth and division), and large rodlike structures (usually 30 to 40 nm in diameter) associated with a small proportion of the bacterial population. No capsule was detected. The cell envelope consisted of four layers: a plasma membrane, a peptidoglycan layer, an outer membrane, and an outermost additional layer. The additional layer was composed of subunits, generally hexagonally packed with center-to-center spacing of 6 to 7 nm. The outer membrane and plasma membrane freeze-fractured through their hydrophobic regions revealing four fracture faces with features similar to those of other gram-negative bacteria. However, some unusual features were seen on the fracture faces of the outer membrane: large raised ring structure (11 to 12 nm in diameter) on cw 3 at the poles of the bacteria; complementary pits or ring-shaped depressions on cw 2; and small raised ring structures (7 to 8 nm in diameter) all over cw 2.     

Medium for Isolation and Growth of Bacteria Associated with Plum Leaf Scald and Phony Peach Diseases

Rickettsia-like bacteria associated with plum leaf scald and phony peach diseases were isolated from diseased but not from healthy tissues and cultured on charcoal-yeast extract medium (BCYE) buffered with ACES (2-[(2-amino-2-oxoethyl) amino]-ethanesulfonic acid). Optimum conditions for isolation and growth on BCYE medium were pH 6.5 to 6.9 at 20 and 25°C under normal atmosphere. Growth of primary colonies and first-passage subcultures was restricted, and colonies reached a maximum diameter of 0.6 mm in 60 days. After 12 passages, subcultures reached maximum growth in 21 days. The rickettsia-like bacteria from BCYE cultures were gram negative, serologically the same as those present in diseased peach and plum, and composed of rod-shaped cells measuring 0.35 by 5 μm (average diameter and maximum length) in a matrix of filamentous strands of similar width but of variable length.     

Persistence length of titin from rabbit skeletal muscles measured with scattering and microrheology techniques

The persistence length of titin from rabbit skeletal muscles was measured using a combination of static and dynamic light scattering, and neutron small angle scattering. Values of persistence length in the range 9-16 nm were found for titin-II, which corresponds to mainly physiologically inelastic A-band part of the protein, and for a proteolytic fragment with 100-nm contour length from the physiologically elastic I-band part. The ratio of the hydrodynamic radius to the static radius of gyration indicates that the proteins obey Gaussian statistics typical of a flexible polymer in a -solvent. Furthermore, measurements of the flexibility as a function of temperature demonstrate that titin-II and the I-band titin fragment experience a similar denaturation process; unfolding begins at 318 K and proceeds in two stages: an initial gradual 50% change in persistence length is followed by a sharp unwinding transition at 338 K. Complementary microrheology (video particle tracking) measurements indicate that the viscoelasticity in dilute solution behaves according to the Flory/Fox model, providing a value of the radius of gyration for titin-II (63 +/- 1 nm) in agreement with static light scattering and small angle neutron scattering results.     

Microbial community structure in autotrophic nitrifying granules characterized by experimental and simulation analyses

This study evaluates the community structure in nitrifying granules (average diameter of 1600 μm) produced in an aerobic reactor fed with ammonia as the sole energy source by a multivalent approach combining molecular techniques, microelectrode measurements and mathematical modelling. Fluorescence in situ hybridization revealed that ammonia-oxidizing bacteria dominated within the first 200 μm below the granule surface, nitrite-oxidizing bacteria a deeper layer between 200 and 300 μm, while heterotrophic bacteria were present in the core of the nitrifying granule. Presence of these groups also became evident from a 16S rRNA clone library. Microprofiles of NH₄⁺, NO₂^–, NO₃^– and O₂ concentrations measured with microelectrodes showed good agreement with the spatial organization of nitrifying bacteria. One- and two-dimensional numerical biofilm models were constructed to explain the observed granule development as a result of the multiple bacteria–substrate interactions. The interaction between nitrifying and heterotrophic bacteria was evaluated by assuming three types of heterotrophic bacterial growth on soluble microbial products from nitrifying bacteria. The models described well the bacterial distribution obtained by fluorescence in situ hybridization analysis, as well as the measured oxygen, nitrite, nitrate and ammonium concentration profiles. Results of this study are important because they show that a combination of simulation and experimental techniques can better explain the interaction between nitrifying bacteria and heterotrophic bacteria in the granules than individual approaches alone.     

Cell surface properties correlated with cohesion in Myxococcus xanthus.

The gliding behavior of Myxococcus xanthus cells is controlled by two multigene systems, A and S, which encode information for adventurous and social behaviors, respectively. The S system can be genetically disrupted through mutation, such as a dsp mutation, or phenotypically disrupted by treating cells with the diazo dye Congo red (Arnold and Shimkets, J. Bacteriol. 170:5765-5770, 1988). One of the functions controlled by the S system is cell agglutination. Immediately after the induction of agglutination, wild-type cells begin to form aggregates, and within 30 min the cells are packed side-to-side in clumps containing thousands of cells. Changes in the cohesive properties of S+ cells are correlated with changes in the topology of the cell surface observed by electron microscopy. Two types of cell-associated appendages were observed on wild-type cells: thin filaments (ca. 5 nm in diameter), which have been called fimbriae or pili, at one cell pole, and thick, flaccid filaments (ca. 50 nm in diameter), referred to as fibrils, at both the sides and tips of cells. Cohesion was correlated with the secretion of the thick fibrils, which coat the cell surface and form an extracellular matrix in which the cells are interconnected. Several lines of evidence suggest that these thick fibrils are involved in cohesion. First, Dsp cells were unable to agglutinate or secrete this extracellular material. Second, wild-type cells which were treated with Congo red neither agglutinated nor secreted the extracellular fibrils. Finally, removal of the Congo red from wild-type cells restored cohesion and also restored production of the thick fibrils. Attempts to estimate the efficiency with which two cells cohered following collision suggested that under optimal conditions, one in three collisions resulted in stable contact. The collision efficiency decreased linearly as the cell density increased, suggesting a cell density-dependent regulation of cohesion. Some aspects of gliding behavior can be explained in terms of an inducer and an inhibitor of S motility.     

Selenium in combination with a tomato lipid extract as a therapy for benign prostatic hyperplasia and its alterations in rats with induced BPH

Benign prostatic hyperplasia (BPH) is the most common adenoma in old men. Tomatoes are a rich source of bioactive compounds that, as well as selenium (Se), possess antioxidant and antiproliferative activity. The aim was to evaluate the therapeutic effect of Se in combination with a tomato extract in aged rats with BPH. Aged male Wistar rats were divided in the following groups (n = 10 rats/group): Control (C), BPH, BPH + Finasteride (BPH + F), BPH + Tomato Lipidic Extract (BPH + E), BPH + Selenium (BPH + S) and BPH plus E plus S (BPH + E + S). After 4 weeks of treatment, prostate weight, diuresis, antioxidants enzymes, prooxidants and inflammatory markers, growth factors and androgens were determined. BPH + E + S reduced prostate weight by 59.29% and inhibited growth by 99.35% compared to BPH + F which only decreased weight and inhibited growth by 15.31% and 57.54%, respectively. Prooxidant markers were higher with BPH + F (49.4% higher vs. BPH), but BPH + E + S decreased these markers (94.27% vs. BPH) and increased antioxidant activity. Finally, diuresis was higher with the BPH + E + S combination and markers of inflammation and growth factors were significantly lower with respect to BPH + F. Our findings provide a beneficial and protective therapeutic option of E + S directed against androgens, oxidative stress and inflammation that regulates cell proliferation in the prostate gland.