Partly melted DNA conformations obtained with a probability peak finding method

Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate the alternative conformations that coexist in equilibrium and the range of their fluctuations. This yields a representation of the conformational ensemble at a given temperature, which is illustrated in a single diagram called a stitch profile. This article describes the methodology and discusses stitch profiles vs. the ordinary probability profiles using the phage lambda genome as an example.Comment: 11 pages, 9 figures; v3: major changes; v4: applications sectio

Problems in Preparation of Chromosomes for Scanning Electron Microscopy to Reveal Morphology and to Permit Immunocytochemistry of Sensitive Antigens

Although much information about chromosome structure and behaviour has been obtained using light microscopy, greater resolution is needed for a thorough understanding of chromosome organisation. Scanning electron microscopy (SEM) can provide valuable data about these three-dimensional organelles. The introduction of methods using osmium impregnation of methanol-acetic acid-fixed chromosome spreads revolutionised matters, producing life-like images of chromosomes. Nevertheless, it became clear that osmium impregnation introduced various artefacts, although the resulting images were still useful. Methanol-acetic acid-fixed chromosomes are, in fact, flattened on the glass substratum, and the 3-dimensional appearance obtained after osmium impregnation is the result of swelling during this process. At the same time, the fibrous substructure of the chromosomes becomes much coarser. More recently a number of alternative methods have become available for studying chromosomes by SEM. Isolated chromosomes, that have not been allowed to dry during preparation, retain a 3-dimensional appearance without osmium impregnation, and the same is true of methanol-acetic acid-fixed chromosomes that have been treated with 45% acetic acid and processed without drying; however, these methods do not permit the routine production of intact metaphase spreads. Use of cytocentrifuge preparations obviates the use of acetic acid fixation and osmium impregnation, produces intact metaphase spreads, and permits the immunocytochemical detection of antigens that are easily destroyed by routine fixation procedures

Gelatin Standards for Elemental Quantification in Biological X-Ray Microanalysis

Standards for X-ray microanalysis (XRMA) can be prepared simply by dissolving measured amounts of gelatin and an appropriate salt in water, dipping grids in the solution, and allowing them to gel and dry. The present study was intended to assess the uniformity, reproducibility, and stability during irradiation of such standards. Visually, the gelatin films appear homogeneous, and XRMA measurements of different grid squares are generally in good agreement. The gelatin standards are susceptible to radiation damage, as judged by several criteria. These are: visible damage; variation of peak/continuum ratios with electron dose; anomalous values obtained with very thin standards; and changes in X-ray counts with prolonged irradiation. In general, the gelatin matrix appears to be lost during irradiation, but the elements within the matrix may be lost at the same rate as the gelatin, or faster, or more slowly

unfixed and fixed human chromosomes show different staining patterns after restriction endonuclease digestion

Restriction endonucleases (REs) have been widely used to produce banding patterns on chromosomes, but it remains uncertain to what extent the patterns are due to the sequence specificity of the enzymes, and to what extent chromatin structure influences the pattern of digestion. To throw light on this question, we have digested with restriction endonucleases unfixed chromosomes prepared in two different ways (isolated, and whole metaphase cells spread with a cytocentrifuge) and compared the results with those obtained on conventionally fixed chromosomes. Unfixed isolated chromosomes are easily destroyed by REs; after fixation with cold methanol, which produced minimal alteration to the chromatin structure, the chromosomes are resistant to the action of REs, and conventional methanol-acetic acid fixation is required to permit the induction of banding patterns by REs. Unfixed cytocentrifuge preparations, in which the chromosomes are still surrounded by cytoplasm, are much more resistant to the action of REs, and again banding patterns were only induced after methanol-acetic acid fixation. We conclude that the action of restriction endonucleases on chromosomes is strongly influenced by chromatin organisation, and that methanol-acetic acid fixation is required to permit the induction of conventional banding patterns on chromosomes

FeH Absorption in the Near-Infrared Spectra of Late M and L Dwarfs

We present medium-resolution z-, J-, and H-band spectra of four late-type dwarfs with spectral types ranging from M8 to L7.5. In an attempt to determine the origin of numerous weak absorption features throughout their near-infrared spectra, and motivated by the recent tentative identification of the E 4\Pi- A ^4\Pi system of FeH near 1.6 microns in umbral and cool star spectra, we have compared the dwarf spectra to a laboratory FeH emission spectrum. We have identified nearly 100 FeH absorption features in the z-, J-, and H-band spectra of the dwarfs. In particular, we have identified 34 features which dominate the appearance of the H-band spectra of the dwarfs and which appear in the laboratory FeH spectrum. Finally, all of the features are either weaker or absent in the spectrum of the L7.5 dwarf which is consistent with the weakening of the known FeH bandheads in the spectra of the latest L dwarfs.Comment: accepted by Ap

Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica.

Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales

Improved Simulation of the Mass Charging for ASTROD I

The electrostatic charging of the test mass in ASTROD I (Astrodynamical Space Test of Relativity using Optical Devices I) mission can affect the quality of the science data as a result of spurious Coulomb and Lorentz forces. To estimate the size of the resultant disturbances, credible predictions of charging rates and the charging noise are required. Using the GEANT4 software toolkit, we present a detailed Monte Carlo simulation of the ASTROD I test mass charging due to exposure of the spacecraft to galactic cosmic-ray (GCR) protons and alpha particles (3He, 4He) in the space environment. A positive charging rate of 33.3 e+/s at solar minimum is obtained. This figure reduces by 50% at solar maximum. Based on this charging rate and factoring in the contribution of minor cosmic-ray components, we calculate the acceleration noise and stiffness associated with charging. We conclude that the acceleration noise arising from Coulomb and Lorentz effects are well below the ASTROD I acceleration noise limit at 0.1 mHz both at solar minimum and maximum. The coherent Fourier components due to charging are investigated, it needs to be studied carefully in order to ensure that these do not compromise the quality of science data in the ASTROD I mission.Comment: 20 pages, 14 figures, submitted to International Journal of Modern Physics

Characterization of disturbance sources for LISA: torsion pendulum results

A torsion pendulum allows ground-based investigation of the purity of free-fall for the LISA test masses inside their capacitive position sensor. This paper presents recent improvements in our torsion pendulum facility that have both increased the pendulum sensitivity and allowed detailed characterization of several important sources of acceleration noise for the LISA test masses. We discuss here an improved upper limit on random force noise originating in the sensor. Additionally, we present new measurement techniques and preliminary results for characterizing the forces caused by the sensor's residual electrostatic fields, dielectric losses, residual spring-like coupling, and temperature gradients.Comment: 11 pages, 8 figures, accepted for publication Classical and Quantum Gravit