The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence.

When the chromatin of Drosophila is examined by digestion with DNAase I or micrococcal nuclease, no general structural organization above the level of the nucleosome is revealed by the cleavage pattern. In contrast, the DNAase I cleavage pattern of specific regions of the Drosophila chromosome shows discrete bands with sizes ranging from a few kilobase pairs (kb) to more than 20 kb. Visualization of such higher order bands was achieved by the use of the Southern blotting technique. The DNAase I-cleaved fragments were transferred onto a nitrocellulose sheet after size fractionation by gel electrophoresis. Hybridization was then carried out with radioactively labeled cloned fragments of DNA from D. melanogaster. For the five different chromosomal regions examined, each gives a unique pattern of higher order bands on the autoradiogram; the patterns are different for different regions. Restriction enzyme cleavage of the fragments generated indicates that the preferential DNAase I cleavage sites in chromatin are position-specific. The chromosomal regions bounded by preferential DNAase I cleavage sites are referred to as supranucleosomal or higher order domains for purposes of discussion and analysis. The micrococcal nuclease cleavage pattern of chromatin at specific loci was also examined. In the one case studied in detail, this nuclease also cleaves at position-specific sites.     

Mapping G-bands on human prophase chromosomes.

OHNUKI's method for demonstrating coils in human metaphase chromosomes also reveals a fine G-band pattern on prophase chromosomes of sufficient clarity to justify an attempt at mapping. Maps are provided for each chromosome to show the maximum number of prophase bands observed, and an intermediate stage in chromosome contraction, tracing the pathways of apparent band fusion as the cell progresses to metaphase, is presented. The prophase bands on many chromosomes tend to occur in distinct groups, the members of which ultimately merge to give the dark G-bands of metaphase chromosomes. Every G-band of the standard metaphase chromosomes. Every G-band of the standard metaphase pattern is compounded from two or more prophase bands. In at least contracted prophase chromosomes examined, some bands are seen which have no obvious metaphase counterpart. There are marked similarities between banded prophases and the chromoomere pattern seen at meiotic prophase. However, since chromosome contraction is a dynamic process, agreement between maps will be expected only for corresponding degrees of chromosome contraction.     

Comparison between high definition FT‐IR,Raman and AFM‐IR for subcellular chemical imaging of cholesteryl esters in prostate cancer cells

The family of vibrational spectroscopic imaging techniques grows every few years and there is a need to compare and contrast new modalities with the better understood ones, especially in the case of demanding biological samples. Three vibrational spectroscopy techniques (high definition Fourier‐transform infrared [FT‐IR], Raman and atomic force microscopy infrared [AFM‐IR]) were applied for subcellular chemical imaging of cholesteryl esters in PC‐3 prostate cancer cells. The techniques were compared and contrasted in terms of image quality, spectral pattern and chemical information. All tested techniques were found to be useful in chemical imaging of cholesterol derivatives in cancer cells. The results obtained from FT‐IR and Raman imaging showed to be comparable, whereas those achieved from AFM‐IR study exhibited higher spectral heterogeneity. It confirms AFM‐IR method as a powerful tool in local chemical imaging of cells at the nanoscale level. Furthermore, due to polarization effect, p‐polarized AFM‐IR spectra showed strong enhancement of lipid bands when compared to FT‐IR.     

Long range periodicities in mouse satellite DNA.

Escherichia coli restriction enzyme II breaks mouse satellite DNA into fragments which form a series of bands on gel electrophoresis. The DNA in the strongest band has a length of 220 to 260 nucleotide pairs and the other bands are multiples of this length. It is shown that these fragments are linked together in long arrays in the satellite sequence. The reassociation register of the DNA is about half the length of the 220 to 260 nucleotide pair fragment. In the electrophoresis pattern of the Eco RII² fragments other weaker bands can be seen. The stronger bands of the minor patterns fall half-way between the bands of the main pattern and the smallest is 120 to 130 nucleotide pairs long. The properties of the minor fragments suggest short spacings of the restriction site which have been produced by unequal crossing-over. The extents of divergence and unequal crossing-over are estimated. From this analysis and the sequence analysis described in the accompanying paper (Biro et al., 1975) it is proposed that mouse satellite DNA consists of an hierarchy of four periodicities which reflect stages in the evolution of the sequence.Digestion of mouse satellite DNA with Hae III produces fragments with the same sizes as those produced by Eco RII, but the yields are much lower. It is suggested that Hae III sites have been introduced by divergence and subsequently spread by unequal crossing-over.     

High-resolution analysis of DNA replication domain organization across an R/G-band boundary.

Establishing how mammalian chromosome replication is regulated and how groups of replication origins are organized into replication bands will significantly increase our understanding of chromosome organization. Replication time bands in mammalian chromosomes show overall congruency with structural R- and G-banding patterns as revealed by different chromosome banding techniques. Thus, chromosome bands reflect variations in the longitudinal structure and function of the chromosome, but little is known about the structural basis of the metaphase chromosome banding pattern. At the microscopic level, both structural R and G bands and replication bands occupy discrete domains along chromosomes, suggesting separation by distinct boundaries. The purpose of this study was to determine replication timing differences encompassing a boundary between differentially replicating chromosomal bands. Using competitive PCR on replicated DNA from flow-sorted cell cycle fractions, we have analyzed the replication timing of markers spanning roughly 5 Mb of human chromosome 13q14.3/q21.1. This is only the second report of high-resolution analysis of replication timing differences across an R/G-band boundary. In contrast to previous work, however, we find that band boundaries are defined by a gradient in replication timing rather than by a sharp boundary separating R and G bands into functionally distinct chromatin compartments. These findings indicate that topographical band boundaries are not defined by specific sequences or structures.     

Studies on human thyroxine-binding globulin. 8. Isoelectric focusing evidence for microheterogeneity of thyroxine-binding globulin

Highly purified thyroxine-binding globulin from pooled human serum homogeneous by conventional criteria, subjected to isoelectric focusing in polyacrylamide gels in a pH gradient from 3–6, produced a pattern of at least nine stainable protein bands. All of these bands appeared to bind thyroxine. Completely desialylated thyroxine-binding globulin subjected to isoelectric focusing produced the same number and pattern of bands located at a different area in the pH gradient. Thyroxine-binding globulin purified from the serum of a single donor was subjected to isoelectric focusing. This thyroxine-binding globulin had the same pattern of protein bands with the exception that one of the major bands seen in the thyroxine-binding globulin from pooled serum was absent. Several possible explanations for these phenomena are discussed.     

Cyclical phenomena occurring during the maturation of the enamel of rat incisor teeth. Their manifestation during drying

A pattern of obliquely oriented bands has been demonstrated at the surface of the maturation zone enamel of freshly dissected rat incisor teeth as they dry. This pattern, of which there is no evidence in the fresh, wet, or completely dry teeth, consists of up to 4 or 5 pale grey, translucent lines separated by wider, whiter, more opaque bands and has been shown to correlate directly with a similar pattern seen on the same teeth after staining with toluidine blue and previously described as the maturation cycle banding pattern (Boyde and Reith 1982). A second pattern comprised of much more closely spaced bands is also described. In this pattern, which again correlates with a similar pattern seen after toluidine blue staining, translucent and opaque bands cross the maturation zone more transversely and have a width of about 200 microns, approximating to 8 h tooth growth. It is postulated that these banding patterns reflect alternately different drying rates of the maturation zone enamel and that they may correspond to cyclical changes in the hydrophobicity and hydrophilicity of enamel matrix both on a daily basis and on a larger time scale.     

Studies on the structure of muscle. III. Phase contrast and electron microscopy of dipteran flight muscle

1. The flight muscles of blowflies are easily dispersed in appropriate media to form suspensions of myofibrils which are highly suitable for phase contrast observation of the band changes associated with ATP-induced contraction. 2. Fresh myofibrils show a simple band pattern in which the A substance is uniformly distributed throughout the sarcomere, while the pattern characteristic of glycerinated material is identical with that generally regarded as typical of relaxed vertebrate myofibrils (A, I, H, Z, and M bands present). 3. Unrestrained myofibrils of both fresh and glycerinated muscle shorten by not more than about 20 per cent on exposure to ATP. In both cases the A substance migrates during contraction and accumulates in dense bands in the Z region, while material also accumulates in the M region. It is proposed that these dense contraction bands be designated the C(z), and C(m) bands respectively. In restrained myofibrils, the I band does not disappear, but the C(z) and C(m) bands still appear in the presence of ATP. 4. The birefringence of the myofibrils decreases somewhat during contraction, but the shift of A substance does not result in an increase of birefringence in the C(z) and C(m) bands. It seems therefore that the A substance, if it is oriented parallel with the fibre axis in the relaxed myofibril, must exist in a coiled or folded configuration in the C hands of contracted myofibrils. 5. The fine structure of the flight muscle has been determined from electron microscopic examination of ultrathin sections. The myofibrils are of roughly hexagonal cross-section and consist of a regular single hexagonal array of compound myofilaments the cores of which extend continuously throughout all bands of the sarcomere in all states of contraction or relaxation so far investigated. 6. Each myofilament is joined laterally with its six nearest neighbours by thin filamentous bridges which repeat at regular intervals along the fibre axis and are present in the A, I, and Z, but not in the H or M bands. When stained with PTA, the myofilaments display a compound structure. In the A band, a lightly staining medullary region about 40 A in diameter is surrounded by a densely staining cortex, the over-all diameter of the myofilament being about 120 A. This thick cortex is absent in the I and H bands, but a thinner cortex is often visible. 7. It is suggested that the basic structure is a longitudinally continuous framework of F actin filaments, which are linked periodically by the lateral bridges (possibly tropomyosin). The A substance is free under certain conditions to migrate to the Z bands to form the C(z) bands. The material forming the C(m) bands possibly represents another component of the A substance. The results do not clearly indicate whether myosin is confined to the A bands or distributed throughout the sarcomere.     

Rapid identification of environmental isolates of Pseudomonas aeruginosa, P. fluorescens and P. putida by SDS-PAGE analysis of whole-cell protein patterns

Abstract Environmental isolates of fluorescent pseudomonads grown to early stationary phase in glucose-enriched Luria broth were treated with proteinase K in sodium dodecylsulphate (SDS) lysis buffer and subsequently analyzed by polyacrylamide gel electrophoresis (PAGE). Four silver-staining protein-fragment bands could be used for rapid identification at the species level. Pseudomonas aeruginosa isolates were easily recognized by a unique banding pattern. Isolates considered to be P. fluorescen from biochemical and physiological tests (classical biotypes I, II, III, IV and V) also had a characteristic banding pattern, which in turn was different from that of P. putida isolates (classical biotype A). A residual group representing intermediate isolates of P. fluorescens (new biotype VI of Barrett et al., J. Gen. Microbiol. 132, 1986) or P. putida (biotype B) had a banding pattern similar to that of classical P. fluorescens biotypes. On the other hand, a group representing other intermediate isolates of P. putida (new biotype C of Barrett et al., J. Gen. Microbiol. 132, 1986) had a unique banding pattern resembling that of classical P. putida biotype A. A small number of protein fragment bands appearing in SDS-PAGE analysis of whole-cell lysates seems adequate for a rapid identification at the species level of P. aeruginosa, P. fluorescens and P. putida isolated from natural environments.     

Typing of Proteus mirabilis from clinical sources by computerized analysis of electrophoretic protein patterns.

Seventy-five strains of Proteus mirabilis (mainly of human origin) were characterized by one-dimensional SDS-PAGE of cellular proteins. The strains came from various countries; 24 were from urine, 17 from faeces (including one from a dog and one from a monkey), 12 from the respiratory tract (including nine from sputum), four from a cerebral abscess, 12 from miscellaneous sources and six from unknown sources. The protein patterns, which contained 45 to 50 discrete bands, were highly reproducible. The patterns of the 75 P. mirabilis cultures plus those of the type strains of six Proteus and Providencia species were used as the basis for two numerical analyses. In the first, which included all the protein bands, the P. mirabilis cultures formed nine clusters at the 85% S level. In the second analysis, in which the principal protein bands (in the 34.0-44.6 kDa range) were excluded, 74 of the 75 cultures of P. mirabilis formed a single cluster at the 77% S level distinct from the six Proteus and Providencia reference strains. The P. mirabilis strain which failed to cluster with the others had a background band pattern typical of the species in the lower molecular weight region but appeared to be less typical in the heavier bands. It is concluded that high resolution PAGE combined with computerized analysis of protein patterns provides the basis for typing clinical strains of P. mirabilis. Reference strains of each of the nine PAGE types identified are available from NCTC for inclusion in future studies.     

Electron microscopic band-interband pattern of polytene chromosomes in Drosophila nasuta albomicans. 2. Salivary gland chromosome 2L.

The band-interband pattern (division 28-52) of salivary gland chromosome 2L in Drosophila nasuta albomicans was studied by light (LM) and electron microscopy (EM) using squash preparations and surface-spread polytene (SSP) chromosome preparations, respectively. LM and EM maps were complied. Based on the digitized EM patterns of five homologous SSP chromosomes a computerized EM chromosome map was plotted. The EM pattern analysis showed a total number of 479 chromosome bands with an almost 83% increase compared with the LM analysis of squash preparations. By extrapolation of the data from 39% of the polytene genome analysed so far in D. n. albomicans, a total number of 2,926 chromosome bands was calculated. This is almost the same number of bands as was calculated earlier for Drosophila hydei using the same SSP chromosome preparation technique. The data in the literature concerning variations in the number of chromosome bands in different Drosophila species, the various chromosome preparation techniques adopted, and the different criteria used for the EM pattern analyses, are discussed.     

Fluorescence analysis of late DNA replication in human metaphase chromosomes.

Thymidine incorporated as a terminal pulse into chromosomes otherwise substituted with 5-bromodeoxyuridine can be detected by associated bright 33258 Hoechst fluorescence. The location of metaphase chromosome regions identified by this method as last to complete DNA synthesis is consistent with the results of autoradiographic analyses with tritiated thymidine. The very late-replicating regions correspond to a subset of those which appear as bands after chromosomes are stained by quinacrine or modified Giemsa techniques. The high resolution of the 33258 Hoechst fluorescence pattern within individual cells is especially useful for revealing variations in the order of terminal replication. Both homolog asynchrony and fluctuations in the distribution of bright 33258 Hoechst fluorescence within chromosomes from different cells are apparent and localized to individual bands. The results are consistent with the possibility that these bands constitute units of chromosome replication as well as structure.     

Investigating the ultrastructure of fibrous long spacing collagen by parallel atomic force and transmission electron microscopy

The ultrastructure of fibrous long spacing (FLS) collagen fibrils has been investigated by performing both atomic force microscopy (AFM) and transmission electron microscopy (TEM) on exactly the same area of FLS collagen fibril samples. These FLS collagen fibrils were formed in vitro from type I collagen and alpha1-acid glycoprotein (AAG) solutions. On the basis of the correlated AFM and TEM images obtained before and after negative staining, the periodic dark bands observed in TEM images along the longitudinal axis of the FLS collagen fibril correspond directly to periodic protrusions seen by AFM. This observation is in agreement with the original surmise made by Gross, Highberger, and Schmitt (Gross J, Highberger JH, Schmitt FO, Proc Natl Acad Sci USA 1954;40:679-688) that the major repeating dark bands of FLS collagen fibrils observed under TEM are thick relative to the interband region. Although these results do not refute the idea of negative stain penetration into gap regions proposed by Hodge and Petruska (Petruska JA, Hodge AJ. Aspects of protein structure. Ramachandran GN, editor. New York: Academic Press; 1963. p. 289-300), there is no need to invoke the presence of gap regions to explain the periodic dark bands observed in TEM images of FLS collagen fibrils.     

The rules for electron microscopic mapping of polytene chromosomes in squashed preparations of Drosophila salivary glands

The following rules of the polytene chromosome mapping at the submicroscopical level are proposed: 1) using anhydrous mixtures of alcohol with acetic acid for fixation of salivary glands which permits to avoid artifacts in the structure of large bands; 2) using sections 120-150 nm thick which improves the revealing of faint bands; 3) including in the analysis larvae being at different stages, since different bands display puffing at different regions; 4) reproducibility of banding pattern in serial sections of some chromosomes. The use of these rules permits to interpret more strictly the observed pictures of the polytene chromosome banding pattern and to avoid possible mistakes of the mapping.     

A comparison of the digestion of nuclei and chromatin by staphylococcal nuclease.

We have followed the kinetics of staphylococcal nuclease digestion of duck reticulocyte nuclei and chromatin from early stages to the digestion limit. We confirm that partial digestion of nuclei produces discrete DNA bands which are multiples of a monomer, 185 base pairs in length. The multimers are shown to be precursors of the monomer, which is next digested to a homogeneous, 140 base pair fragment. This fragment in turn gives rise to an array of nuclear limit digest DNA bands, which is almost identical with the limit digest pattern of isolated chromatin. As in the case of chromatin, half the DNA of nuclei is acid soluble at this limit. While the DNA limit digest patterns of nuclei and chromatin are similar, the large multimeric structures present as intermediates in nuclear digestion are absent in chromatin digestion. Alternate methods of chromatin gel preparation appear to leave more of the higher order structure intact, as measured by the production of these multimeric bands. Our results are consistent with the "beads on a string" model of chromatin proposed by others.     

Folding-unfolding of FN-III domains in tenascin: an elastically coupled two-state system

In a single-molecule atomic force microscopy (AFM) experiment, the tenascin molecule is stretched by an external force causing an elongation which is due to the unfolding of the FN-III modules. The features of the force-extension curves depend on the pulling speed and show a saw-tooth pattern (lower speeds) or a smooth pattern (higher speeds). In any case, the unfolded domains are elastically coupled to the unfolded modules, acting as transmitters of the external force. In this communication, the folding-unfolding process of the FN-III domains in tenascin is studied using reaction rate theory and a simple two-state model. The main hypothesis of the study is that, at microscopic level, the force needed to unfold a domain and the unfolding rate (unfolding velocity) can mimic the macroscopic process of measurement by AFM. As the external force is applied, the probability of unfolding increases as dictated by the reaction rate theory. Within this context, a relationship between the unfolding force and the unfolding velocity is obtained. The latter relation will describe microscopically the process in a phenomenological fashion. Moreover, while relating the results of this study with other experimental (AFM measurements) and theoretical (Monte Carlo simulations) data, we found that the graph of unfolding force-unfolding velocity is similar to that of external force-pulling velocity. The refolding process can also be studied within this model and the results show similar trends. The latter suggests a generic and universal behavior of such kind of molecular domains at least in the light of the proposed model.     

Characterization of spelt (Triticum spelta L.) forms by gel electrophoretic analyses of seed storage proteins. I. The gliadins

A comparison betweeen the electropherograms of the spelt and wheat cultivars showed specific differences in the gliadin band patterns which provided the possibility of a clear classification into spelt or wheat. A special nomenclature was developed to be able to improve the presentation of the gliadin band pattern of spelt, which is different from that of wheat. This nomenclature, however, has not yet been applied to other cereals. The gliadin band patterns were presented in a schematic form. As a parameter for comparison, idealized band patterns of both wheat and spelt were developed by comparing the proportions of the bands of all available types. When comparing the gliadin band patterns of the spelt cross-breeds with their corresponding parental generations, it was noted that the same parental bands were not always transmitted and that the cross-breeds showed differences in the intensity, mobility, occurrence, and the splitting of single bands. In general it can be said that the band pattern of the daughter generation – even in the examined and generations – is more similar to the band pattern of the mother than to that of the father, which proves a maternal effect. Received: 29 June 1996 / Accepted: 12 July 1996     

STUDIES ON THE STRUCTURE OF MUSCLE : III. PHASE CONTRAST AND ELECTRON MICROSCOPY OF DIPTERAN FLIGHT MUSCLE

1. The flight muscles of blowflies are easily dispersed in appropriate media to form suspensions of myofibrils which are highly suitable for phase contrast observation of the band changes associated with ATP-induced contraction. 2. Fresh myofibrils show a simple band pattern in which the A substance is uniformly distributed throughout the sarcomere, while the pattern characteristic of glycerinated material is identical with that generally regarded as typical of relaxed vertebrate myofibrils (A, I, H, Z, and M bands present). 3. Unrestrained myofibrils of both fresh and glycerinated muscle shorten by not more than about 20 per cent on exposure to ATP. In both cases the A substance migrates during contraction and accumulates in dense bands in the Z region, while material also accumulates in the M region. It is proposed that these dense contraction bands be designated the C_z, and C_m bands respectively. In restrained myofibrils, the I band does not disappear, but the C_z and C_m bands still appear in the presence of ATP. 4. The birefringence of the myofibrils decreases somewhat during contraction, but the shift of A substance does not result in an increase of birefringence in the C_z and C_m bands. It seems therefore that the A substance, if it is oriented parallel with the fibre axis in the relaxed myofibril, must exist in a coiled or folded configuration in the C hands of contracted myofibrils. 5. The fine structure of the flight muscle has been determined from electron microscopic examination of ultrathin sections. The myofibrils are of roughly hexagonal cross-section and consist of a regular single hexagonal array of compound myofilaments the cores of which extend continuously throughout all bands of the sarcomere in all states of contraction or relaxation so far investigated. 6. Each myofilament is joined laterally with its six nearest neighbours by thin filamentous bridges which repeat at regular intervals along the fibre axis and are present in the A, I, and Z, but not in the H or M bands. When stained with PTA, the myofilaments display a compound structure. In the A band, a lightly staining medullary region about 40 A in diameter is surrounded by a densely staining cortex, the over-all diameter of the myofilament being about 120 A. This thick cortex is absent in the I and H bands, but a thinner cortex is often visible. 7. It is suggested that the basic structure is a longitudinally continuous framework of F actin filaments, which are linked periodically by the lateral bridges (possibly tropomyosin). The A substance is free under certain conditions to migrate to the Z bands to form the C_z bands. The material forming the C_m bands possibly represents another component of the A substance. The results do not clearly indicate whether myosin is confined to the A bands or distributed throughout the sarcomere.