Tissue-specific and light-dependent changes of chromatin organization in barley (Hordeum vulgare)

The DNase I sensitivity of the nuclear genes encoding the NADPH-protochlorophyllide oxidoreductase, the light-harvesting chlorophyll a/b protein (LHCP), the hordeins and a 15-kDa protein of unknown function was assayed in chromatin of etiolated and green leaves and endosperm tissue of barley (Hordeum vulgare L.). A tissue-specific differentiation of chromatin structure was found for the LHCP, hordein and 15-kDa protein genes. The genes for the LHCP and the 15-kDa protein, which are expressed in leaf tissue, display DNase I sensitivity in leaves but not in endosperm. Hordein genes which are expressed solely in endosperm, were insensitive to low levels of digestion with DNase I in leaves but sensitive in endosperm. The effect of light on chromatin structure was determined by comparing leaves of etiolated plants and plants which had been grown under a day/night cycle. Only in the case of the 15-kDa protein is there a remarkable change from a DNAse-I-sensitive configuration in etiolated leaves to a more resistant one in leaves from illuminated plants. The gene for the NADPH-protochlorophyllide oxidoreductase was found to be equally sensitive to DNase I in leaves and endosperm.     

Synthesis of the intranuclear crystals in Scolopendrium vulgare (L.) SM

Proteinaceous intranuclear crystals are found in the fern Scolopendrium vulgare. During mitosis these crystals are eliminated from the nucleus into the cytoplasm, where they are dissolved. New crystals appear in the nucleus. The site of synthesis of intranuclear crystal proteins was investigated using quantitative ultrastructural autoradiography after incubation with tritiated lysine. The results suggest a migration of cytoplasmic proteins to the nucleus, part of which would then be incorporated into the intranuclear crystals.     

Cholesteric organization of DNA in the stallion sperm head

The fine structure of chromatin in sperm heads was investigated by different microscopic techniques: in vivo examinations in the polarizing microscope, thin sections and freeze-fracture replicas observed by transmission electron microscopy. The freeze-fractured chromatin appears to be formed of superimposed lamellae, each one 330 A thick. These lamellae are parallel to the flattening plane of the sperm head. This situation was already described in other mammal spermatozoa and in particular in the bull and the rabbit. This work presents a new interpretation of this lamellated aspect. The chromatin structure of these spermatozoa is that of a cholesteric liquid crystal. This structure resembles that of a plywood, made of superimposed layers of parallel filaments, but instead of having a right angle between two successive layers, there is a progressive rotation and similar orientation occurs at each 180 degrees rotation. The apparent lamellae result from cleavages due to freeze-fracture between levels of parallel filament orientation. The thickness of lamellae corresponds therefore to the half helicoidal pitch of the cholesteric liquid crystal. This model is consistent with our observations by polarizing microscopy. The lamellation is not visible in thin sections of stallion spermatozoa. There are however biochemical methods to decondense chromatin and we are able to observe this lamellation in sections normal to the flattening plane of sperm heads. The methods used classically to decondense the sperm chromatin lead to extremely varied aspects which are discussed, some of them being closely related to the structure of cholesteric liquid crystals.     

In vitro decondensation of the sperm chromatin in Holothuria tubulosa (sea cucumber) not affecting proteolysis of basic nuclear proteins

Sea urchin and sea star oocyte extracts contain proteolytic activities that are active against sperm basic nuclear proteins (SNBP). This SNBP degradation has been related to the decondensation of sperm chromatin as a possible model to male pronuclei formation. We have studied the presence of this proteolytic activity in Holothuria tubulosa (sea cucumber) and its possible relationship with sperm nuclei decondensation. The mature oocyte extracts from H. tubulosa contain a proteolytic activity to SNBP located in the macromolecular fraction of the egg‐jelly layer. SNBP degradation occurred both on sperm nuclei and on purified SNBP, histones being more easily degraded than protein Ø_o (sperm‐specific protein). SNBP degradation was found to be dependent on concentration, incubation time, presence of Ca²⁺, pH, and this activity could be a serine‐proteinase. Thermal denaturalization of the oocyte extracts (80°C, 10–15 min) inactivates its proteolytic activity on SNBP but does not affect sperm nuclei decondensation. These results would suggest that sperm nuclei decondensation occurs by a mechanism different from SNBP degradation. Thus, the sperm nuclei decondensation occurs by a thermostable factor(s) and the removal of linker SNBP (H1 and protein Ø_o) will be a first condition in the process of sperm chromatin remodeling.     

Structural organization of the meiotic prophase chromatin in the rat testis

Pachytene nuclei were isolated from rat testes by the unit gravity sedimentation technique and contained histone variants H1a, H1t, TH2A, TH2B, and X2 in addition to the somatic histones H1bde, H1c, H2A, H2B, H3, and H4. The basic organization of the pachytene chromatin namely the nucleosome repeat length and the accessibility to micrococcal nuclease, was similar to that of rat liver interphase chromatin. However, when digested by DNase I, the susceptibility of pachytene chromatin was 25% more than liver chromatin under identical conditions. Nucleosome core particles were isolated from both liver and pachytene nuclei and were characterized for their DNA length and integrity of the nucleoprotein on low ionic strength nucleoprotein gels. While liver core particles contained all the somatic histones H2A, H2B, H3, and H4, in the pachytene core particles, histone variants TH2A, X2, and TH2B had replaced nearly 60% of the respective somatic histones. A comparison of the circular dichroism spectra obtained for pachytene and liver core particles indicated that the pachytene core particles were less compact than the liver core particles. Studies on the thermal denaturation properties of the two types of core particles revealed that the fraction of the pachytene core DNA melting at the premelting temperature region of 55-60 degrees C was significantly higher than that of the liver core DNA.     

Nucleosomal organization of chromatin in sperm nuclei of the bivalve mollusc Aulacomya ater

The sperm nuclei of Aulacomya ater, family Mitylidae, contain three proteins (X, Aa5 and Aa6) which are specific to this cell type coexisting with a set of five somatic-type histones. Information about the chromatin structure resulting from this kind of association is scarce. Therefore, we have probed the structure of this sperm chromatin through digestion with micrococcal nuclease in combination with salt fractionation. The data obtained have allowed us to propose a nucleosomal arrangement for this chromatin. However, two types of nucleosomes would be present in agreement with their protein components.     

Image analysis of the chromatin organization in the nuclear domains of freeze fractured hepatocytes and lymphocytes

The complex organization of the interphase nucleus can be analyzed, by way of thin sectioning and also freeze-fracture. This approach has previously been utilized in association with image analysis to quantitatively describe the organization of isolated rat liver nuclei and nuclear matrices. The main nuclear domains which, in section, present marked differences due to their electron-density, can be identified in replicas with more complex procedures, based on the quantitative evaluation of the number of particles per unit area and mainly by using image analysis. A quantitative analysis of the nuclear substructures has been performed by way of image analysis on in situ nuclei of freeze-fractured cells presenting marked differences in the heterochromatin quantity, such as hepatocytes and lymphocytes. The replicated nuclear particles have been classified according to their diameter and the obtained histograms have been quantitatively evaluated. The nuclear domains, heterochromatin, interchromatin, nucleolus, present characteristic ratios among the three main classes of particles; that is, ribonucleoproteins, solenoid filaments and solenoid fibre aggregates. The typical patterns of the nuclear domains can be further stressed by selecting a single class of particles and by examining its topographic localization. While interchromatin and nucleolar domains present a similar quantitative pattern in hepatocytes and lymphocytes, the heterochromatin of lymphocytes contains a significative higher percentage of solenoid aggregates than that of hepatocytes.     

Nucleosomal organization of a part of chromatin in mollusc sperm nuclei with a mixed basic protein composition

The structural organization of mature sperm chromatin from three representatives of theMytilidae family has been studied. The acid-soluble proteins in these species nuclei are primarily sperm-specific (approximately 80%) with the remainder being core histones. Previously, we have shown that the mature sperm nuclei of these molluscs are compact, dense structures formed by interaction of the spermspecific proteins with DNA (1). Here we show that: a) although the histones are minor chromatin protein fraction, they still organize a part (20–25%) of the total DNA into nucleosomes; b) one of the sperm-specific proteins, different from somatic H1 or H5 histones participates in the formation of the beaded structures.     

Evaluation of DNA fragmentation in llama (Lama glama) sperm using the sperm chromatin dispersion test

The integrity of sperm chromatin is now viewed as an important factor in male fertility and in early embryonic development. The objectives of this study were: (1) adapt the simple and inexpensive sperm chromatin dispersion (SCD) test to evaluate DNA fragmentation in llama sperm and establish the halo patterns observed in this species, (2) determine an effective and reliable positive control for this technique and (3) evaluate correlation between the SCD test and the toluidine blue (TB) stain. To adapt the SCD test, three different mercaptoethanol (ME) concentrations were assayed (2.5%, 5% and 10% ME). To determine an effective positive control, three treatments (incubation at 100 °C for 30 min, incubation with 0.3 M NaOH for 30 min at room temperature and exposure to UV light for 2h) were assayed. The concentration selected to use in the SCD test was 5% ME, because it produced the largest halo while still conserving the structure of the core. Four DNA dispersion patterns were clearly observed: (I) nuclei with large DNA dispersion halos; (II) nuclei with medium halos; (III) nuclei with very small halos and (IV) nuclei with no halo. All treatments used as positive controls were effective in producing DNA fragmentation. A high correlation (r=0.84, P=0.03) was observed between spermatozoa without halos and TB positive cells. To conclude, SCD patterns in llama sperm have been established as well as a repeatable positive control for the assay. The SCD test and TB stain are simple and inexpensive techniques that can be used to evaluate DNA damage in llama sperm.     

Ultrastructure of the spermatozoid of Lycopodium obscurum (Lycopodiaceae)

Ultrastructural observations reveal that the spermatozoid of Lycopodium obscurum is crescent shaped and contains two posteriorly directed flagella that are inserted at the front of the cell. The nucleus is broad and elongated with a narrow posterior projection or nuclear diverticulum. Spline microtubules (MTs) number 180 at their maximum and provide the framework for the cell. These MTs extend from the anterior of the locomotory apparatus and along the outermost surface of the nucleus, with a central shank of 14–17 MTs encircling the cell for at least one-third gyre beyond the nucleus. The two basal bodies are slightly staggered and positioned at the front of the cell over a highly elongated multilayered structure (MLS). The MLS extends laterally around the cell anterior and curves posteriorly over the nucleus. One large anterior mitochondrion is situated subjacent to the MLS, while numerous small mitochondria are scattered near or among the lobes of the single plastid. The plastid rests on the inner nuclear surface and contains numerous large starch grains. This cell differs from that of L. cernuum, the only other species of Lycopodium examined to date, in that it is more elongated and has an anterior-posterior orientation of the nucleus, basal bodies, MLS, and spline. Comparisons with coiled gametes of bryophytes and Selaginella suggest that some degree of coiling and cell streamlining may be ancestral in archegoniate spermatozoids.     

Structural transitions in short-chain lipid assemblies studied by (31)P-NMR spectroscopy

The self-assembled supramolecular structures of diacylphosphatidylcholine (diC(n)PC), diacylphosphatidylethanolamine (diC(n)PE), diacylphosphatidyglycerol (diC(n)PG), and diacylphosphatidylserine (diC(n)PS) were investigated by (31)P nuclear magnetic resonance (NMR) spectroscopy as a function of the hydrophobic acyl chain length. Short-chain homologs of these lipids formed micelles, and longer-chain homologs formed bilayers. The shortest acyl chain lengths that supported bilayer structures depended on the headgroup of the lipids. They increased in the order PE (C(6)) < PC (C(9)) < or = PS (C(9) or C(10)) < PG (C(11) or C(12)). This order correlated with the effective headgroup area, which is a function of the physical size, charge, hydration, and hydrogen-bonding capacity of the four headgroups. Electrostatic screening of the headgroup charge with NaCl reduced the effective headgroup area of PS and PG and thereby decreased the micelle-to-bilayer transition of these lipid classes to shorter chain lengths. The experimentally determined supramolecular structures were compared to the assembly states predicted by packing constraints that were calculated from the hydrocarbon-chain volume and effective headgroup area of each lipid. The model accurately predicted the chain-length threshold for bilayer formation if the relative displacement of the acyl chains of the phospholipid were taken into account. The model also predicted cylindrical rather than spherical micelles for all four diacylphospholipid classes and the (31)P-NMR spectra provided evidence for a tubular network that appeared as an intermediate phase at the micelle-to-bilayer transition. The free energy of micellization per methylene group was independent of the structure of the supramolecular assembly, but was -0.95 kJ/mol (-0.23 kcal/mol) for the PGs compared to -2.5 kJ/mol (-0.60 kcal/mol) for the PCs. The integral membrane protein OmpA did not change the bilayer structure of thin (diC(10)PC) bilayers.     

Chlorophyll organization in dark-grown and light-grown pine (Pinus brutia) and barley (Hordeum vulgare)

A study was conducted comparing the organization of chlorophyll during development of the photosynthetic apparatus in dark-grown and light-grown pine and barley. The rationale was that gymnosperms, but not angiosperms, have a capacity to synthesize chlorophyll in darkness. Seedlings of Pinus brutia were germinated and grown in darkness or under photoperiodic (day/night) conditions. The low-temperature (77 K) fluorescence spectra of newly-emerging dark-grown seedlings exhibited a single fluorescence band peaking at 678–679 nm, which decayed primarily with a ∼5.5 ns lifetime. Over the first few days of growth, the emission shifted to longer wavelengths and a subnanosecond lifetime component became prevalent. After several days of dark growth the emission spectrum and lifetime profile of the low temperature fluorescence came to resemble those of light-grown pine and barley. At room temperature, dark-grown pine showed little variable fluorescence, though addition of DCMU caused a substantial fluorescence rise. Illumination with moderate light for a few hours was sufficient to 'photoinduce' the appearance of normal variable fluorescence. At 77 K, DCMU-treated samples clearly showed a very long-lived (∼40 ns) fluorescence lifetime component in light-grown pine and barley. This component was undetectable in dark-grown pine. If, however, dark-grown samples were illuminated either before or after DCMU addition and then frozen to 77 K, the ∼40 ns lifetime component appeared at a fluorescence intensity similar to that in light-grown samples. These results are explained primarily in terms of photoactivation of the photosystem II (PSII) donor side. The temporary maintenance of PSII in an inactive, highly-quenched state is suggested to provide an available, yet protected precursor for active PSII.     

Structural organization of the fibrin(ogen) alpha C-domain

We hypothesized that the alpha C-domain of human fibrinogen (residues hA alpha 221-610) and of other species consists of a compact COOH-terminal region (hA alpha 392-610) and a flexible NH(2)-terminal connector region (hA alpha 221-391) which may contain some regular structure [Weisel and Medved (2001) Ann. N.Y. Acad. Sci. 936, 312-327]. To test this hypothesis, we expressed in E. coli recombinant fragments corresponding to the full-length human alpha C-domain and its NH(2)- and COOH-terminal regions as well as their bovine counterparts, bA alpha 224-568, bA alpha 224-373, and bA alpha 374-568(538), respectively, and tested their folding status by fluorescence spectroscopy, circular dichroism (CD), and differential scanning calorimetry (DSC). All three methods revealed heat-induced unfolding transitions in the full-length bA alpha 224-568 and its two COOH-terminal fragments, indicating that the COOH-terminal portion of the bovine alpha C-domain is folded into a compact cooperative structure. Similar results were obtained by CD and DSC with the full-length and the COOH-terminal h392-610 human fragments. The NH(2)-terminal fragments of both species, b224-373 and h221-392, did not exhibit any sign of a compact structure. However, their heat capacity functions, CD spectra, and temperature dependence of ellipticity at 222 nm were typical for peptides in the extended helical poly(L-proline) type II conformation (PPII), suggesting that they contain this type of regular structure. This is consistent with the presence of proline-rich tandem repeats in the sequence of both bovine and human connector regions. These results indicate that both bovine and human fibrinogen alpha C-domains consist of a compact globular cooperative unit attached to the bulk of the molecule by an extended NH(2)-terminal connector region with a PPII conformation.     

Structural organization of chromatin as a factor determining the rate of its endonucleolysis in irradiated and nonirradiated thymocytes

A study was made of chromatin endonucleolysis in hypotonic thymocytes incubated in digestive buffers containing different concentrations of potassium, magnesium, calcium, and mercaptoethanol. Inhibition of endonucleolysis by univalent cation during the first 20 min of incubation was followed by intensive chromatin degradation. A decrease in free potassium content retarded chromatin degradation and enhanced the inhibiting effect of the univalent cations. The regularities of changes in the rate of chromatin endonucleolysis in different digestive buffers were similar with both exposed and intact thymocytes.     

Structural organization of the copulation site in the medfly Ceratitis capitata (Diptera: Tephritidae) and observations on sperm transfer and storage

The copulation site of the medfly Ceratitis capitata was investigated at anatomical and ultrastructural levels. It consists of the anterior vagina, with a ventral fertilization chamber and a dorsal insemination pocket into which the two spermathecal ducts open. The fertilization chamber is an organ comprised of a number of alveoli that in virgin females are filled with a filamentous secretion, whereas in mated females contain sperm bundles. Through study of the internal morphology of the aedeagus, its position in the anterior vagina, and the direct observation of sperm transfer and storage, we confirmed that sperm are ejaculated through two gonopores at the top of the distiphallus and another at the base of the genital rod. The sperm flow dorsally into the insemination pocket and ventrally into the fertilization chamber. During copulation, the two spermathecae and the fertilization chamber are progressively filled with spermatozoa.     

Tightly-bound form of poly(ADP-ribose)polymerase in the higher order of chromatin organization

A tightly-bound form of poly(ADP-ribose)polymerase is present, within the third level of rat testis chromatin structure, both in the loops and in chromatin matrix. When chromatin matrix was extensively digested with DNAaseI, only little residual enzymatic activity remained in the insoluble fraction, the extent of DNA hydrolysis being well correlated to the progressive loss of the poly(ADP-ribose)polymerase activity. These findings suggest that the tightly-bound form of the enzyme is not an intrinsic protein component of chromatin matrix but is only indirectly located in this structure, being rather associated to the attachment points of loop DNA on the matrix.     

Structural organization of the gills in pipefish (Teleostei,Syngnathidae)

Summary The morphology and structural features of the gills of the two Western Baltic pipefish Nerophis ophidion and Syngnathus rostellatus were investigated using scanning electron microscopy. The general anatomy of the gills complies with the general pattern in fish. Several adaptations though, show the highly specialized nature of pipefish gills. The filaments are extremely short, few in number and carry only a few lamellae due to the limited space in the branchial cavity. The lamellae have a widely projecting form yet still have a small area in comparison to other fish. Gill irrigation is performed by a specialized pumping mechanism which forces respiratory water through the small but densely packed gill sieve. Although both species live in the same habitat and belong to the same family, differences in gill morphology were found and are related to different lifestyles. S. rostellatus is the more active species and therefore has more filaments per gill arch, more lamellae per filament, wider projecting lamellae and a more extreme utilisation of available space in the gill cavity through a very densely packed gill sieve. N. ophidion has a stationary mode of life and therefore has a less extreme gill anatomy.     

Structural organization of chromatin in nucleolar organizer regions of nucleoli with a nucleolonema-like and compact ribonucleoprotein distribution

We have studied the relationship between the structural organization of intranucleolar chromatin and fibrillar nucleolar structures, fibrillar centers, and RNP fibrillar component, which are the interphase counterpart of metaphase nucleolar organizer regions (NORs), in regenerating rat hepatocytes and in a human tumor cell line (TG cells). These two cell types were characterized by a nucleolonema-like and compact nucleolar RNP distribution, respectively. We found that, in sections selectively stained for DNA, the intranucleolar chromatin composed of extended, nonnucleosomal DNA filaments formed roundish agglomerates with a spatial distribution which was superimposable on that of the fibrillar centers and the RNP fibrillar component around them and on sites of the silver reaction in samples selectively stained for Ag-NOR proteins. The agglomerates of extended nonnucleosomal DNA filaments were small and numerous in regenerating hepatocyte nucleoli, in which the RNP components had a nucleolonema-like distribution, whereas they were large and few in TG cell nucleoli, in which the RNP components showed a compact organization. Since the pattern of ribosomal RNA synthesis and processing was similar in the two cell types, a model was proposed in which the difference in size and shape of the agglomerates of extended DNA might be responsible for the different structural organization of the RNP components.     

Structural organization of the retina in the tree shrew (Tupaia glis)

This investigation was undertaken to establish the gross and ultrastructural organization of the photoreceptors and retina in the Malayan tree shrew (Tupaia glis). Photographs of the fundus revealed no specialization or differentiation of a central foveal region. Histologic sections revealed a single row of relatively short and thick cones distributed uniformly throughout the retina. Electron micrographs of the retina indicated that the receptor outer segments are closely invested by pigment-filled epithelial processes and an amorphous interstitial material. The internal fine structure of the receptor outer segments revealed the characteristic stacks or arrays of bimembranous discs. The ellipsoid portions of the cone inner segments include tightly packed and extraordinarily large mitochondria. These mitochondria consist of unique patterns of concentric cristae arranged in highly ordered whorls of lamellar configurations. The cone synaptic pedicles contain a unique system of tubules not previously described in synaptic endings. Histologic sections indicated that only cone populations are located in the central region of the retina, whereas histologic, histochemical, and ultrastructural comparisons suggested that photoreceptors with some "rodtype" features are located more peripherally. The relatively small proportion of these rodtype receptors among the great preponderance of cone populations is in general accord with the tree shrew's diurnal habits as well as its great reliance on photopic vision and its visually guided behavior.     

Structure of lipoprotein (a) studied by spin-labeling

The potent tumor promoter 12-O-tetradecanoylphorbol 13-acetate causes a 2-fold increase in 1,2-diacylglycerol levels within 15–30 min in cultured chick embryo differentiated myoblasts. The weak tumor promoter 12-O-decanoylphorbol 13-acetate was 250 times less effective and the non-promoter 4-α-phorbol 12,13 didecanoate was ineffective at producing this response. During subcellular fractionation, the stimulated portion of the diacylglycerol was distributed similarly to the plasma membrane fraction. Evidence is presented that this diacylglycerol originates from pre-existing lipid rather than from $\text{de}\text{novo}$ synthesis. Possible implications of these findings with regard to the inhibition of myoblast fusion by the tumor promoter are discussed.