Subunit organization of Euglena chromatin

Digestion of $\text{Euglena}$ nuclei or extracted chromatin with micrococcal nuclease results in the identification of a repeating structure. The DNA repeat size, analyzed on agarose and polyacrylamide gels, is found to be 225±13 base pairs. DNase I digestion produces a serie of fragments multiples of roughly 10 bases. Eventhough pressure shearing is necessary to disrupt the though pellicule of the phytoflagellate, we confirm that, in $\text{Euglena}$, chromatin organization is similar to that of other eukaryotes.     

Histone-histone associations within chromatin. Cross-linking studies using tetranitromethane.

Treatment of chromatin with the protein cross-linker tetranitromethane (TNM) results in a product identified as an F2a1-F2b dimer. The same product appears after treatment with TNM of HeLa cells growing in culture. Furthermore acid-extracted histones which have been fractionated into the five separate species can be recombined and mixed with DNA to produce a nucleohistone preparation which is also cross-linked by TNM to give the F2a1-F2b dimer. F1 and F3 can be excluded from the reconstitution mixture without effect on the dimer production. In contrast, the presence of F2a2 is essential to the proper reconstitution of F2a1 and F2b with DNA. The specificity of TNM and the characteristics of the reaction suggest that F2a1 and F2b are cross-linked at their specific binding sites. These results provide evidence that F2a1, F2a2, and F2b interact specifically in chromatin.     

Low-angle neutron scattering from chromatin subunit particles.

Monomer chromatin particles containing 140 base pairs of DNA and eight histone molecules have been studied by neutron scattering. From measurements in various H2O/D2O mixtures, radii of gyration and the average scattering density of the particle were determined. The radius of gyration under conditions when scattering from the DNA dominates is 50A, and when scattering from the protein dominates, 30A. Consequently the core of the particle is largely occupied by the histones while the outer shell consists of DNA together with some of the histone.     

Subunit structure of alpha-satellite DNA containing chromatin from African green monkey cells.

alpha-Satellite DNA containing chromatin from African green monkey cells (CV-1 cells) has been used to study the question whether or not nucleosomes are arranged in phase with the 172 bp repeat unit of the satellite DNA. Digestion experiments with DNAase II led us to exclude a simple phase relationship between the nucleosomal and the satellite DNA repeats. Digestion of CV-1 nuclei with micrococcal nuclease and endogenous nuclease (s) produced a series of sharp bands in the satellite DNA register over a background of heterogeneous length fragments. This observation is explained by a preferential cleavage of certain nucleotide sequences by these nucleases and is not in contradiction to our conclusion that a simple phase relationship does not exist.     

Electron microscopy of chromatin subunit particles

Electron microscope studies of PS-particles obtained by partial nuclease digestion of calf thymus chromatin shows them to be very similar in size and shape to particles which have been detected in native chromatin. Furthermore, measurement of the spacing between pairs of such particles, together with the known length of the DNA coiled in the particles gives an estimate of about 200 base pairs for the chromatin “subunit”.     

Reversibility of the low-salt transition of chromatin core particles.

The low-salt transition of chromatin core particles is reversible if the monovalent cation concentration is kept above 0.2 mM. Exposure of the particles to salt concentrations below this value results in a nonreversible secondary transition. The nonreversible changes are relatively slow with a half-time of about 15 minutes. Once exposed to such low ionic strength, the particles then begin to refold with increasing salt in at least two steps over a much higher ionic strength range than is required for the usual low-salt transition. The refolding is very fast, with a half-time less than a minute. Small differences between particles which had or had not been exposed to very low salt persist even when the particles are returned to near physiological ionic strengths.     

Effects of pH on the stability of chromatin core particles.

Chromatin core particles near physiological ionic strength undergo a reversible transition induced by changes in pH near neutrality. While sedimentation studies indicate no significant effect on size or shape, changes in tyrosine fluorescence anisotropy and in circular dichroism suggest a somewhat looser structure at high pH. Further support of this suggestion is given by high salt dissociation experiments; at pH 8 core particles begin to show changes at lower salt concentration than at pH 6. The pH transition appears unaffected by the presence of Mg2+ but can be blocked by crosslinking of the histones. A possible relationship is suggested between this transition and increases in intracellular pH which correlate with enhancement in several aspects of cellular activity including DNA replication.     

Retrotransposon-gene associations are widespread among D. melanogaster populations

We have surveyed 18 natural populations of Drosophila melanogaster for the presence of 23 retrotransposon-gene-association alleles (i.e., the presence of an LTR retrotransposon sequence in or within 1,000 bp of a gene) recently identified in the sequenced D. melanogaster genome. The identified associations were detected only in the D. melanogaster populations. The majority (61%) of the identified retrotransposon-gene associations were present only in the sequenced strain in which they were first identified. Thirty percent of the associations were detected in at least one of the natural populations, and 9% of the associations were detected in all of the D. melanogaster populations surveyed. Sequence analysis of an association allele present in all populations indicates that selection is a significant factor in the spread and/or maintenance of at least some of retroelement-gene associations in D. melanogaster.     

Interaction of a tryptophan-containing peptide with chromatin core particles. A fluorescence study

The binding of a tetrapeptide lysyltryptophylglycyllysine to nucleosome core particles has been investigated using UV absorption and fluorescence spectroscopy. Modifications of the absorption spectra and fluorescence quenching of the tryptophyl residue are consistent with stacking between the indole ring and nucleic acid bases. Therefore DNA interactions with histones do not prevent stacking of the tryptophyl residue with nucleic acid bases in the peptide-core particle complexes. The number of peptide binding sites is reduced to half that of naked DNA.     

Salt induced transitions of chromatin core particles studied by tyrosine fluorescence anisotropy.

Chromatin core particles containing 146 base pairs of DNA have been found to undergo a single defined transition below 10 mM ionic strength as studied by both sedimentation velocity and tyrosine fluorescence anisotropy. A method is described for the preparation of such core particles from chicken erythrocytes with greater than 50% yield.     

Protein distribution amongst chromatin particles following DNAse II digestion

When active chromatin is released as a Mg-soluble fraction following digestion of nuclei with DNAse II, as concomitant release of HMG proteins, and hnRNP particles occurs. Release of HMG 14 and 17 is dependent on active chromatin release, whereas HMG 1 and 2, and hnRNP particles are released in an independent process. The Mg-soluble fraction comprises a heterogenous mixture of particles of less compact conformation than normal nucleosomes, and prone to protein-induced aggregation. Histone H1, and HMG 14 and 17 appear to be associated with these particles in a reversible manner, whereas HMG 1 and 2 are unbound.     

Homologous and non-homologous chromosome associations by interchromosomal chromatin connectives in Ornithogalum virens

Based on interchromosomal chromatin connectives, a statistical analysis of homologous and non-homologous chromosome associations was made on mitotic metaphase chromosomes of Ornithogalum virens. The great majority of connectives involve constitutive heterochromatin, and connections between homologous chromosomes are twice as common as would be expected by chance. It is suggested that constitutive heterochromatin with similar DNA is involved in both homologous and non-homologous chromosome associations.     

Comparative study of nucleosome particles in chromatin from normal and tumor cells. I. Structural parameters

The composition and structure of nucleosomic fragments isolated from the ascitic hepatoma 22A cells, liver and from cells of C3HA mice in norm and after partial hepatectomy were investigated. Via electrophoresis in 1.5% agarose gel with the emplogment of reperic restrictive DNA fragments and with the help of mathematical processing, the value of the nucleosomic DNA repeat in ascitic hepatoma 22A was calculated to be 187 b.p., and in regenerating liver--196 b.p. The absence of the H1 degree subfraction in chromatin of ascitic hepatoma 22A cells was found. Lower electrophoretic mobility in 5% polyacrylamid gel of nucleosomic chromatin fragments of ascitic hepatoma 22A as compared with their counterparts from healthy mice liver was established. The method of circular dichroism allowed to reveal differences in the RNA and protein structural state in nucleosomes of normal and tumour cells. The structure of nucleosomes of regenerating mice liver of the C3HA strain did not differ from that of normal liver of the same mice.     

Subunit composition of goblet-shaped particles from the cell wall of Flexibacter polymorphus

Submicroscopic goblet-shaped particles ( goblets ) were released from the cell envelope of the marine gliding bacterium Flexibacter polymorphus when treated with the nonionic detergent Triton X-100 followed by sonication. The goblets were purified by cesium chloride density gradient centrifugation and exhibited an equilibrium buoyant density of 1.30 g/mL at 23 degrees C. They were composed of protein and a small amount of carbohydrate (approximately 3.4% by weight). Aqueous suspensions exhibited an absorption maximum in the ultraviolet at a wavelength of 276 nm and a smaller shoulder at 281 nm. Phospholipids were not detected in purified preparations of goblets , though they are known to be prominent constituents of the intact membranes of this microbe. Polyacrylamide gel electrophoresis of goblets solubilized in sodium dodecyl sulfate and 2-mercaptoethanol indicated four major polypeptide components ranging in molecular weight from 13 000 to 80 000. This number of different protein subunits corroborates earlier ultrastructural observations indicating a multisubunit composition.     

Weak climatic associations among British plant distributions

Aim Species distribution models (SDMs) are used to infer niche responses and predict climate change‐induced range shifts. However, their power to distinguish real and chance associations between spatially autocorrelated distribution and environmental data at continental scales has been questioned. Here this is investigated at a regional (10 km) scale by modelling the distributions of 100 plant species native to the UK. Location UK. Methods SDMs fitted using real climate data were compared with those utilizing simulated climate gradients. The simulated gradients preserve the exact values and spatial structure of the real ones, but have no causal relationships with any species and so represent an appropriate null model. SDMs were fitted as generalized linear models (GLMs) or by the Random Forest machine‐learning algorithm and were either non‐spatial or included spatially explicit trend surfaces or autocovariates as predictors. Results Species distributions were significantly but erroneously related to the simulated gradients in 86% of cases (P < 0.05 in likelihood‐ratio tests of GLMs), with the highest error for strongly autocorrelated species and gradients and when species occupied 50% of sites. Even more false effects were found when curvilinear responses were modelled, and this was not adequately mitigated in the spatially explicit models. Non‐spatial SDMs based on simulated climate data suggested that 70–80% of the apparent explanatory power of the real data could be attributable to its spatial structure. Furthermore, the niche component of spatially explicit SDMs did not significantly contribute to model fit in most species. Main conclusions Spatial structure in the climate, rather than functional relationships with species distributions, may account for much of the apparent fit and predictive power of SDMs. Failure to account for this means that the evidence for climatic limitation of species distributions may have been overstated. As such, predicted regional‐ and national‐scale impacts of climate change based on the analysis of static distribution snapshots will require re‐evaluation.     

Interspecific associations among larval helminths in fish

Various processes can generate associations between the larvae of different helminth species in their fish intermediate or paratenic host. We investigated the pairwise associations among larval helminth species in eight different fish populations, using two different coefficients of associations, in order to determine in what situations they are strongest. All helminth species included use the fish studied as either their second intermediate host or their paratenic host, and are acquired by the fish when it ingests an infected first intermediate host. The intensity of infection correlated positively with fish length for most helminth species. Pairs of species which both exhibited positive correlations with fish length tended to be more strongly associated with one another, although this tendency was not pronounced. Similarity in life cycle had a more important influence on pairwise associations. Among the 62 pairwise associations that could be computed, pairs of helminth species that shared both first intermediate hosts and definitive hosts were the most strongly associated, followed by pairs that shared only one other host, and finally by pairs that did not share other hosts. The results suggest that assemblages of larval helminth parasites in fish are not random collections of locally available species, but rather structured packets of larval parasites that travel together along common transmission routes.