bluuebunny/crossref_metadata_2025 huggingface dataset:
Competence, determination, and meristemoid plasticity in tobacco organogenesis in vitro
Authors: Dhaliwal Harbinder S , Ramesar-Fortner Nicole S , Yeung Edward C , Thorpe Trevor A
Published: July 2003

Tobacco leaf explants can produce both shoots and roots depending on the phytohormones in the medium. These arise directly via meristemoids (meristematic centers), which form distinct primordia and then organs. In this study it was found that shoot primordia arose from the palisade mesophyll cells at the adaxial surface, while root primordia arose from the rib parenchyma cells, near the existing vascular bundles. In studies on competency and determination, it was found that the tobacco leaf explants required 46 days in culture on a shoot-inducing medium (SIM) to become determined for shoot formation, while the explants were competent for rooting at excision and needed only 1 day on the root-inducing medium (RIM) to become determined for root formation. Transfer of explants from SIM or RIM to basal medium (BM without phytohormones) and vice versa supported the above findings. Transfer of explants from SIM to RIM and vice versa, delayed the timing of root and shoot formation, but not the position in the explant from which the organs arose. On transfer from SIM to RIM or vice versa, meristemoids that were already determined for shoot or root formation continued to develop, while those not yet determined were inhibited and (or) reverted to parenchymatous tissue. Thus under our culture conditions meristemoids in tobacco leaf explants are not plastic.Key words: competence, determination, meristemoid plasticity, organogenesis, tobacco.
Phosphorus concentration and pH in decaying wood affect establishment of the red-listed moss Buxbaumia viridis
Authors: Wiklund Karin
Published: July 2003

Many red-listed species grow on decaying wood in the boreal forest, and their persistence depends on dispersal to new patches. To investigate whether substrate quality could affect establishment and distribution of the red-listed moss Buxbaumia viridis (DC) Moug. & Nestl., cultivation experiments as well as a field investigation of wood quality were performed. Spore germination was negatively affected by low pH and phosphorus (P) concentration in cultivation media, while nitrogen (N) concentration did not significantly affect germination. Results from the experiments were supported by the field investigation, where the probability of sporophyte occurrence increased with increasing pH. In addition, the interaction between substrate type (wood or humus) and P was significant. Occurrence of sporophytes was not significantly affected by N concentration in the wood. The results from the cultivation experiments and the field study imply that the safe site for germination and establishment of Buxbaumia viridis is either a substrate with continuously high moisture or a substrate with lower moisture but with increased pH and (or) P content, attained, e.g., by throughfall and litterfall from deciduous trees, and that non-optimal pH, P, and moisture conditions could restrict establishment and distribution of the species.Key words: bryophyte, decaying wood, germination, protonema, safe site, substrate quality.
The pattern of seed development and maturation in beach pea (Lathyrus maritimus)
Authors: Chinnasamy Gurusamy , Bal Arya Kumar
Published: July 2003

The developmental patterns of seed, seed coat, and hardseededness were studied in naturally growing crop plants of beach pea (Lathyrus maritimus (L.) Bigel.) at six reproductive growth stages (S1S6). Grass pea (Lathyrus sativus L.) seeds were used for comparison in some experiments. The accumulation of fresh and dry weight in pod shell and seed of beach pea and pod shell of grass pea followed an almost sigmoidal pattern. However, grass pea seed showed a linear pattern of weight accumulation. During maturation, moisture content of pod shells and seeds decreased because of dehydration. Beach pea seeds were able to germinate precociously at S4. Seeds collected between S1 and S3 failed to germinate because of immaturity, whereas the development of hard seed coats prevented germination in seeds gathered at S5 and S6. An imbibition test revealed that hardseededness completely prevented water absorption of S5 and S6 seeds even after 24 days of soaking. In grass pea, precocious seed germination was observed at S3. However, speed of germination, germination percentage, seedling length and dry weight increased as seeds approached maturity. Lipid and protein accumulation in seeds of both species increased progressively with maturity and showed a positive correlation with seed weight accumulation. In both beach pea and grass pea seeds, S6 was identified as a physiological maturity stage.Key words: beach pea, grass pea, hard seed, imbibition, Lathyrus, seed coat, seed development, water impermeability.
Multiple mechanisms for seed dormancy regulation in shadscale (Atriplex confertifolia: Chenopodiaceae)
Authors: Garvin Susan C , Meyer Susan E
Published: July 2003

Shadscale (Atriplex confertifolia (Torr. & Frem.) Wats.) is a dominant shrub species of western North American deserts. Its one-seeded utricles are enclosed in bracteoles, and its seeds are highly dormant at dispersal. We examined the role of soluble inhibitors, bracteole effects, after-ripening, and chilling in regulating dormancy for six shadscale populations. Seeds in bracteole-enclosed fruits required chilling to become germinable, and the fraction responsive to chilling was small for recently harvested seeds. This fraction increased during dry storage for 24 weeks, but the rate of increase decreased asymptotically. After-ripening rate was an exponential function of storage temperature over the range 2250°C. After-ripening models based on these nonlinear relationships for each of four seed populations accounted for 96% of the change in the chilling-responsive fraction during 3 years of laboratory storage. Rate of change in the chilling-responsive fraction during laboratory storage was log-linearly related to the chilling-responsive fraction for recently harvested seeds. Excision of utricles from recently harvested fruits increased the chilling-responsive fraction but did not generally eliminate the chilling requirement. Leaching or dewinging to remove soluble inhibitors increased germination of otherwise nondormant seeds but did not relieve primary dormancy. Knowledge of dormancy loss mechanisms will facilitate prediction of germination phenology and seed bank persistence for shadscale under fluctuating field conditions.Key words: after-ripening, germination, saltbush, soluble inhibitor, stratification, thermal time.
New species of Trichoderma from Asia
Authors: Bissett John , Szakacs George , Nolan Carol Ann , Druzhinina Irina , Gradinger Cornelia , Kubicek Christian P
Published: July 2003

Seven new species of Trichoderma, isolated from soil or tree bark from Siberia, Nepal, northern India, Taiwan, Thailand, Cambodia, and Malaysia, are described based on morphological and physiological characters, and from their phylogenetic position inferred from parsimony analyses of nucleotide sequences of the internal transcribed spacer (ITS) regions of the rDNA cluster (ITS1 and 2) and partial sequences of translation elongation factor 1-alpha (tef1α). Trichoderma sinensis sp. nov. and Trichoderma effusum sp. nov. are additions to Trichoderma section Longibrachiatum. Trichoderma helicum sp. nov., Trichoderma rossicum sp. nov., Trichoderma velutinum sp. nov., and Trichoderma cerinum sp. nov. are additions to section Pachybasium. Trichoderma erinaceum sp. nov. is described in section Trichoderma. The contribution of sequence data in resolving species in Trichoderma is demonstrated by Trichoderma helicum, which is morphologically indistinguishable from Trichoderma tomentosum Bissett, even though the two species are not phylogenetically closely related.Key words: Hypocrea, systematics, taxonomy, phylogeny.
Effects of achene dimorphism on dormancy and progeny traits in the two ephemerals Hedypnois cretica and Crepis aspera (Asteraceae)
Authors: El-Keblawy Ali
Published: July 2003

Hedypnois cretica (L.) Dum.-Cours. and Crepis aspera L. are ephemeral composites native to the Mediterranean coastal desert of Sinai, Egypt, with marked achene dimorphism. This study examined the relationship between achene morphology and both some progeny traits and germination behaviour in terms of final germination percentage and germination speed. The effects of length of achene storage and temperature of storage on germination behaviour were particularly examined. Fresh harvested seeds showed little germination. After 6 months of storage, central achenes attained higher germination percentages in the two species and germinated faster in C. aspera than the peripheral achenes. The dormancy loss was faster in achenes of H. cretica than in those of C. aspera. Greater germination dimorphism was associated with greater dimorphism in size and morphology and consequently in the dispersal ability of the two morphs of C. aspera than in H. cretica. Warm storage significantly enhanced the germination level and speed of the heavier peripheral achenes compared with those of the central achenes of both species, so this was dependent on storage period. Plants produced by peripheral achenes had a significantly greater size than those from central achenes. This difference was more pronounced in H. cretica and persisted until 70 days postemergence but disappeared after 40 days in C. aspera. Results are discussed in light of possible adaptive significance and selective forces, such as the differential dispersal, dormancy, and growth of the two morphs, that maintain the dimorphism in the unpredictable heterogeneous deserts.Key words: achene dimorphism, Asteraceae, dormancy, germination, storage temperature.
Spectral reflectance characteristics of Pinus radiata needles affected by dothistroma needle blight
Authors: Stone Christine , Chisholm Laurie A , McDonald Simon
Published: July 2003

Dothistroma needle blight, caused by Dothistroma septosporum (Dorog) Morelet, is an economically significant disease of several Pinus species in New Zealand, Australia, Chile, South Africa, and parts of Asia, North America, and Europe. The spectral reflectance properties of Pinus radiata D. Don needles infected by D. septosporum were examined over the visible and near-infrared wavelength region (4001000 nm). The largest reflectance difference occurred on the shoulder of the near-infrared region at 763 nm. Wavelengths of greatest sensitivity to D. septosporum infection were located in the ranges of 675691 nm, followed by wavelengths near 760 and 550 nm. Sensitivity minima occurred at 434, 493, 506, 709, and 1373 nm. The reflectance ratio best correlated to needle damage was 709/691 nm (r = 0.739, P < 0.001). Among the other reflectance indices tested, an index based on wavelengths of the upper red edge (710740 nm) was also well correlated (r = 0.730, P < 0.001). There was not a strong linear relationship between the point of maximum slope in the red edge region (red edge position) and needle damage category. This may be because D. septosporum is a necrotrophic fungal pathogen producing a complex series of damage symptoms: initial chlorosis, production of red and brown metabolites, rapid loss of cellular integrity, cell necrosis, and eventual desiccation. Diagnostic features identified in the infected needle spectra may contribute to the formulation of remotely sensed spectral indices for detecting and monitoring dothistroma needle blight in plantations.Key words: Dothistroma, Pinus radiata, needle damage, reflectance spectra, remote sensing.
Complex tendril branching in two species ofParthenocissus: implications for the vitaceous shoot architecture
Authors: Wilson Trevor , Posluszny Usher
Published: July 2003

This study compares the developmental morphology of Parthenocissus quinquefolia Planch. (L.) (Virginia creeper) with that of Parthenocissus tricuspidata (Sieb. & Zucc.) Planch. (Boston ivy) to better understand how the tendril is related to the main shoot architecture of the Vitaceae. Tendril development is looked at from inception to maturity using scanning electron microscopy and epi-illumination microscopy. A tendril primordium is initiated low on the periphery of a shoot apical meristem; this pattern of development is reminiscent of typical monopodial shoot development. A tendril "shoot" in turn produces several bract-opposed branches and resembles the main shoot in its early development. However, a tendril develops through lateral growth, and because it lacks lateral buds, its architecture appears more sympodial than the main shoot. As more tendril branches are produced, the tendril "shoot" pattern of development gradually changes to a pattern of development reported in other vitaceous tendrils. This shift in development suggests how other vitaceous tendrils may be related to the shoot. Because tendril development in Parthenocissus can be demonstrated to be sympodial, it lends evidence to the idea that the unique monopodial-like system in members of the Vitaceae may be derived. The main shoot and tendril development are more similar than has previously been shown.Key words: Vitaceae, Parthenocissus, monopodial, sympodial, tendril, development.
A geographically diverse set of isolates indicates two phylogenetic lineages withinStachybotrys chartarum
Authors: Koster Brenda , Scott James , Wong Bess , Malloch David , Straus Neil
Published: July 2003

Stachybotrys chartarum is a black mitosporic fungus capable of dense colonization of cellulose-based building materials such as drywall. The presence of S. chartarum in indoor environments has been reported as linked to a variety of alleged environment-related illnesses including infant acute idiopathic pulmonary hemorrhage, although there continues to be insufficient (especially exposure) data to support such associations. We investigated genetic variation among 52 morphologically and geographically diverse, indoor and outdoor isolates of S. chartarum sensu lato using molecular markers based on β-tubulin, calmodulin, elongation factor-1 alpha, and trichodiene synthase genes, as well as the internal transcribed spacer region of nuclear ribosomal DNA. Gene genealogies proved concordant in dividing all isolates into two strongly supported clades. The majority of the variable sites separating these lineages were fixed within each of these clades, and there was no evidence of recombination between genotypes. The results of this study therefore provide strong support for the recognition of two phylogenetic species within S. chartarum sensu lato, and further demonstrate the limitations of morphological characters in delineating monophyletic taxa among morphologically simple fungi.Key words: Stachybotrys atra, cryptic speciation, calmodulin, elongation factor-1 alpha, trichodiene synthase.
Decaisnella formosa sp. nov. (Ascomycota, Massariaceae) from an Australian sandy beach
Authors: Abdel-Wahab M A , Jones E B.G
Published: July 2003

Decaisnella formosa sp. nov., an undescribed ascomycete, was discovered on intertidal wood from a beach on the Mornington Peninsula, National Park, Victoria, Australia. Of the eleven species described under the genus Decaisnella, none match D. formosa, which is described here as a new species.Key words: Loculoascomycetes, Melanommatales, marine fungi, muriform ascospores.
Development of the flower and inflorescence of Arum italicum (Araceae)
Authors: Barabé Denis , Lacroix Christian , Gibernau Marc
Published: July 2003

The spadix of Arum italicum Miller consists of two main parts: a clavate sterile portion (appendix) and a cylindroid fertile portion. In the fertile portion with both male and female zones, there are two zones of sterile flowers (bristles). The basal portion of bristles is surrounded by a verrucose structure consisting of a mass of tissular excrescences. During early stages of development, there is no free space between the different zones of the inflorescence. The elongation of the inflorescence axis is what eventually separates the different zones from each other. There are no atypical flowers that are morphologically intermediate between male and female flowers as is the case in other genera of Aroideae (e.g., Cercestis, Philodendron, Schismatoglottis). The structure of the bristles in the inflorescences of Arum does not correspond to any type of atypical flower (unisexual or bisexual) that has been analysed previously in the Araceae. From a developmental point of view, it is not possible to determine if the bristles correspond to aborted or modified female or male flowers. In the early stages of development, the stamens, staminodes, and appendix are covered by globular masses of extracellular calcium oxalate crystals.Key words: development, unisexual flowers, gradient, calcium oxalate crystals.
Examination of EmrE conformational differences in various membrane mimetic environments
Authors: Federkeil Sandra L , Winstone Tara L , Jickling Glen , Turner Raymond J
Published: July 2003

Ethidium multidrug resistance protein (EmrE) is a member of the small multidrug resistance family of proteins and is responsible for resistance in Escherichia coli to a diverse group of lipophilic cations. Research is beginning to elucidate structural information as well as substrate binding and extrusion mechanisms for this protein. However, the choice of membrane mimetic environment to perform structural studies needs to be made. In this study EmrE was solubilized in different membrane mimetic environments to investigate the influence of environment on the structure and dynamics of the protein by comparing the fluorescence properties of emission maxima, peak shifts, relative intensities, acrylamide quenching constants, and polarization. Taken together, the different fluorescence observations on EmrE in the various membrane mimetic systems tested suggest that the tryptophan residues in EmrE are present in the most flexible and exposed state when solubilized in methanol, followed by sodium dodecyl sulfate and urea. The two detergents N-dodecyl-β-D-maltoside (DM) and polyoxyethylene(8)dodecyl ether, for the most part, only display subtle differences between the spectral properties with DM best representing the lipid environment. The conformation of EmrE is clearly more open and dynamic in detergent relative to being reconstituted in small unilamellar vesicles. The fluorescence observations of EmrE solubilized in trifluoroethanol shows an environment that is similar to that of EmrE solubilized in detergents. Additionally, secondary structure was monitored by circular dichroism (CD). The CD spectra were similar among the different solubilizing conditions, suggesting little difference in α-helical content. This work establishes groundwork for the choice of solubilizing conditions for future structural, folding, and ligand binding studies.Key words: SMR, EmrE, tryptophan fluorescence, membrane proteins, detergent solubilization, membrane mimetic.
ESI-MS and FTIR studies of the interaction between the second PDZ domain of hPTP1E and target peptides
Authors: Papp Robert , Ekiel Irena , English Ann M
Published: July 2003

The specificity of interaction between the second PDZ domain of human protein tyrosine phosphatase1E (PDZ2) and a C-terminal peptide, ENEQVSAV, from the guanine nucleotide exchange factor RA-GEF-2 was investigated using Fourier transform infrared (FTIR) spectroscopy and electrospray ionization mass spectrometry (ESI-MS). Specificity of the binding interaction and the importance of Ser in the 2 position of the target peptide were demonstrated using alternate peptides ENEQVCAV and KDDEVYYV. FTIR-monitored thermal denaturation in the amide I region showed a 10°C increase in melting temperature (Tm) for the PDZ2-ENEQVSAV complex compared with that of free PDZ2, and the spectra revealed increased absorption in the β-sheet region (1628 cm1) of PDZ2 on peptide binding. Neither of these results were observed with peptides containing either Cys or Tyr in the 2 position. Complex formation with the Ser-containing peptide was further demonstrated by direct measurement of a 1:1 PDZpeptide complex by ESI-MS in 100% aqueous solutions without the need for organic co-solvents. Our results demonstrate that even a single atom (O [Formula: see text] S) substitution from Ser to Cys in the 2 position disrupts C-terminal peptide binding to PDZ2.Key words: PDZ2 from hPTP1E, ESI-MS, FTIR, ligand binding.
High concentration of DNA in condensed chromatin
Authors: Daban Joan-Ramon
Published: July 2003

The lengths of the DNA molecules of eukaryotic genomes are much greater than the dimensions of the metaphase chromosomes in which they are contained during mitosis. From this observation it has been generally assumed that the linear packing ratio of DNA is an adequate measure of the degree of DNA compaction. This review summarizes the evidence suggesting that the local concentration of DNA is more appropriate than the linear packing ratio for the study of chromatin condensation. The DNA concentrations corresponding to most of the models proposed for the 3040 nm chromatin fiber are not high enough for the construction of metaphase chromosomes. The interdigitated solenoid model has a higher density because of the stacking of nucleosomes in secondary helices and, after further folding into chromatids, it yields a final concentration of DNA that approaches the experimental value found for condensed chromosomes. Since recent results have shown that metaphase chromosomes contain high concentrations of the chromatin packing ions Mg2+and Ca2+, it is discussed that dynamic rather than rigid models are required to explain the condensation of the extended fibers observed in the absence of these cations. Finally, considering the different lines of evidence demonstrating the stacking of nucleosomes in different chromatin complexes, it is suggested that the face-to-face interactions between nucleosomes may be the driving force for the formation of higher order structures with a high local concentration of DNA.Key words: chromosomes, metaphase chromosomes, chromatin, chromatin higher order structure, DNA.
Models for chromatin remodeling: a critical comparison
Authors: Holde K van , Yager T
Published: July 2003

Nucleosome remodeling has been shown, in many cases, to involve cis displacement of nucleosomes on the DNA. This process seems similar to the long-recognized random diffusion of nucleosomes along DNA, but the remodeling process is unidirectional and ATP dependent. Several years ago, we developed a model for nucleosome migration, based on the diffusion of "twist-defects" within the nucleosomal DNA. This has been modified into a model that incorporates ATP-dependent defect generation, and can account for many observations concerning remodeling. However, certain experimental studies in recent years have cast doubt on the applicability of the twist-diffusion model for remodeling, and seem to favor instead a "reptation" model. We discuss herein these problems and propose a resolution.Key words: nucleosome, remodeling, chromatin.
Getting into chromatin: how do transcription factors get past the histones?
Authors: Morse Randall H
Published: July 2003

Transcriptional activators and the general transcription machinery must gain access to DNA that in eukaryotes may be packaged into nucleosomes. In this review, I discuss this problem from the standpoint of the types of chromatin structures that these DNA-binding proteins may encounter, and the mechanisms by which they may contend with various chromatin structures. The discussion includes consideration of experiments in which chromatin structure is manipulated in vivo to confront activators with nucleosomal binding sites, and the roles of nucleosome dynamics and activation domains in facilitating access to such sites. Finally, the role of activators in facilitating access of the general transcriptional machinery to sites in chromatin is discussed. Key words: nucleosome, chromatin, transcriptional activation, Saccharomyces cerevisiae.
HMGN dynamics and chromatin function
Authors: Catez Frédéric , Lim Jae-Hwan , Hock Robert , Postnikov Yuri V , Bustin Michael
Published: July 2003

Recent studies indicate that most nuclear proteins, including histone H1 and HMG are highly mobile and their interaction with chromatin is transient. These findings suggest that the structure of chromatin is dynamic and the protein composition at any particular chromatin site is not fixed. Here we discuss how the dynamic behavior of the nucleosome binding HMGN proteins affects the structure and function of chromatin. The high intranuclear mobility of HMGN insures adequate supply of protein throughout the nucleus and serves to target these proteins to their binding sites. Transient interactions of the proteins with nucleosomes destabilize the higher order chromatin, enhance the access to nucleosomal DNA, and impart flexibility to the chromatin fiber. While roaming the nucleus, the HMGN proteins encounter binding partners and form metastable multiprotein complexes, which modulate their chromatin interactions. Studies with HMGN proteins underscore the important role of protein dynamics in chromatin function.Key words: HMG, nuclear proteins, chromatin, HMGN.
Revisiting the structure and functions of the linker histone C-terminal tail domain
Authors: Lu Xu , Hansen Jeffrey C
Published: July 2003

Linker histones stabilize folded chromatin, acting through their long C-terminal tails. The C-termini contain high percentages of evenly distributed lysine and arginine residues and have no secondary structure in solution. Hence, it has generally been believed that the C-termini function by shielding negative charges on the DNA backbone. However, recent evidence supports a mechanism of action of the linker histone C-terminus that involves formation of specific secondary structure(s) upon interaction with other components of the chromatin fiber.Key words: linker histones, chromatin folding, charge neutralization, secondary structure.
Characteristics of γ-H2AX foci at DNA double-strand breaks sites
Authors: Pilch Duane R , Sedelnikova Olga A , Redon Christophe , Celeste Arkady , Nussenzweig Andre , Bonner William M
Published: July 2003

Phosphorylated H2AX (γ-H2AX) is essential to the efficient recognition and (or) repair of DNA double strand breaks (DSBs), and many molecules, often thousands, of H2AX become rapidly phosphorylated at the site of each nascent DSB. An antibody to γ-H2AX reveals that this highly amplified process generates nuclear foci. The phosphorylation site is a serine four residues from the C-terminus which has been evolutionarily conserved in organisms from giardia intestinalis to humans. Mice and yeast lacking the conserved serine residue demonstrate a variety of defects in DNA DSB processing. H2AXΔ/Δ mice are smaller, sensitive to ionizing radiation, defective in class switch recombination and spermatogenesis while cells from the mice demonstrate substantially increased numbers of genomic defects. γ-H2AX foci formation is a sensitive biological dosimeter and presents new and exciting opportunities to understand important biological processes, human diseases, and individual variations in radiation sensitivity. These potentialities demonstrate the importance of understanding the parameters and functions of γ-H2AX formation.
Xenopustranscription factor IIIA and the 5S nucleosome: development of a useful in vitro system
Authors: Yang Zungyoon , Hayes Jeffrey J
Published: July 2003

5S RNA genes in Xenopus are regulated during development via a complex interplay between assembly of repressive chromatin structures and productive transcription complexes. Interestingly, 5S genes have been found to harbor powerful nucleosome positioning elements and therefore have become an important model system for reconstitution of eukaryotic genes into nucleosomes in vitro. Moreover, the structure of the primary factor initiating transcription of 5S DNA, transcription factor IIIA, has been extensively characterized. This has allowed for numerous studies of the effect of nucleosome assembly and histone modifications on the DNA binding activity of a transcription factor in vitro. For example, linker histones bind 5S nucleosomes and repress TFIIIA binding in vitro in a similar manner to that observed in vivo. In addition, TFIIIA binding to nucleosomes assembled with 5S DNA is stimulated by acetylation or removal of the core histone tail domains. Here we review the development of the Xenopus 5S in vitro system and discuss recent results highlighting new aspects of transcription factor  nucleosome interactions.Key words: nucleosomes, 5S genes, transcription factor IIIA, chromatin.
HMGA proteins: flexibility finds a nuclear niche?
Authors: Reeves Raymond
Published: July 2003

The mammalian HMGA family of chromatin proteins possesses an unusual constellation of physical, biochemical, and biological characteristics that distinguish them from other nuclear proteins. Principal among these is the fact that, unlike other proteins, they possess little detectable secondary structure prior to interactions with other macromolecules (DNA, RNA, proteins). Upon binding to substrates, however, the HMGA proteins undergo specific disordered-to-ordered structural transitions and also induce alterations in the structure of the substrates themselves. Their intrinsic structural flexibility, combined with other features such as the control of their substrate interactions via complex patterns of in vivo biochemical modifications, allows the HMGA proteins to actively participate in a wide variety of nuclear activities including DNA replication, DNA repair, chromatin remodeling, control of gene transcription, and regulation of mRNA processing.Key words: chromatin, gene activation, high performance liquid chromatography, HMG-I(Y), mass spectrometry, transcription.
A haploid affair: core histone transitions during spermatogenesis
Authors: Lewis John D , Abbott D Wade , Ausió Juan
Published: July 2003

The process of meiosis reduces a diploid cell to four haploid gametes and is accompanied by extensive recombination. Thus, the dynamics of chromatin during meiosis are significantly different than in mitotic cells. As spermatogenesis progresses, there is a widespread reorganization of the haploid genome followed by extensive DNA compaction. It has become increasingly clear that the dynamic composition of chromatin plays a critical role in the activities of enzymes and processes that act upon it. Therefore, an analysis of the role of histone variants and modifications in these processes may shed light upon the mechanisms involved and the control of chromatin structure in general. Histone variants such as histone H3.3, H2AX, and macroH2A appear to play key roles in the various stages of spermiogenesis, in addition to the specifically modulated acetylation of histone H4 (acH4), ubiquitination of histones H2A and H2B (uH2A, uH2B), and phosphorylation of histone H3 (H3p). This review will examine recent discoveries concerning the role of histone modifications and variants during meiosis and spermatogenesis.Key words: histone variants, histone modifications, chromatin structure, meiosis.
The complex interactions of p53 with target DNA: we learn as we go
Authors: Kim Ella , Deppert Wolfgang
Published: July 2003

The most import biological function of the tumor suppressor p53 is that of a sequence-specific transactivator. In response to a variety of cellular stress stimuli, p53 induces the transcription of an ever-increasing number of target genes, leading to growth arrest and repair, or to apoptosis. Long considered as a "latent" DNA binder that requires prior activation by C-terminal modification, recent data provide strong evidence that the DNA binding activity of p53 is strongly dependent on structural features within the target DNA and is latent only if the target DNA lacks a certain structural signal code. In this review we discuss evidence for complex interactions of p53 with DNA, which are strongly dependent on the dynamics of DNA structure, especially in the context of chromatin. We provide a model of how this complexity may serve to achieve selectivity of target gene regulation by p53 and how DNA structure in the context of chromatin may serve to modulate p53 functions.Key words: tumor suppressor p53, sequence-specific DNA binding, DNA conformation, chromatin, chromatin remodeling.
Micromechanics of chromatin and chromosomes
Authors: Marko John F , Poirier Michael G
Published: July 2003

The enzymes that transcribe, recombine, package, and duplicate the eukaryotic genome all are highly processive and capable of generating large forces. Understanding chromosome function therefore will require analysis of mechanics as well as biochemistry. Here we review development of new biophysical-biochemical techniques for studying the mechanical properties of isolated chromatin fibers and chromosomes. We also discuss microscopy-based experiments on cells that visualize chromosome structure and dynamics. Experiments on chromatin tell us about its flexibility and fluctuation, as well as quantifying the forces generated during chromatin assembly. Experiments on whole chromosomes provide insight into the higher-order organization of chromatin; for example, recent experiments have shown that the mitotic chromosome is held together by isolated chromatin-chromatin links and not a large, mechanically contiguous non-DNA "scaffold".Key words: DNA struture, chromatin, chromosomes, mitosis.
Magnetic tweezers: a sensitive tool to study DNA and chromatin at the single-molecule level
Authors: Zlatanova Jordanka , Leuba Sanford H
Published: July 2003

The advent of single-molecule biology has allowed unprecedented insight into the dynamic behavior of biological macromolecules and their complexes. Unexpected properties, masked by the asynchronous behavior of myriads of molecules in bulk experiments, can be revealed; equally importantly, individual members of a molecular population often exhibit distinct features in their properties. Finally, the single-molecule approaches allow us to study the behavior of biological macromolecules under applied tension or torsion; understanding the mechanical properties of these molecules helps us understand how they function in the cell. In this review, we summarize the application of magnetic tweezers (MT) to the study of DNA behavior at the single-molecule level. MT can be conveniently used to stretch DNA and introduce controlled levels of superhelicity into the molecule and to follow to a high definition the action of different types of topoisomerases. Its potential for chromatin studies is also enormous, and we will briefly present our first chromatin results.Key words: single-molecules, chromatin, topoisomerases, magnetic tweezers, force.
Histone H1 and the dynamic regulation of chromatin function
Authors: Brown David T
Published: July 2003

Eukaryotic DNA is organized in a complex structure called chromatin. Although a primary function of chromatin is compaction of DNA, this must done such that the underlying DNA is potentially accessible to factor-mediated regulatory responses. Chromatin structure clearly plays a dominant role in regulating much of eukaryotic transcription. The demonstration that reversible covalent modification of the core histones contribute to transcriptional activation and repression by altering chromatin structure and the identification of numerous ATP-dependent chromatin remodeling enzymes provide strong support for this view. Chromatin is much more dynamic than was previously thought and regulation of the dynamic properties of chromatin is a key aspect of gene regulation. This review will focus on recent attempts to elucidate the specific contribution of histone H1 to chromatin-mediated regulation of gene expression.Key words: histone H1, chromatin, gene expression.
A role for poly(ADP-ribosyl)ation in DNA methylation
Authors: Zardo Giuseppe , Reale Anna , Matteis Giovanna De , Buontempo Serena , Caiafa Paola
Published: July 2003

The aberrant DNA methylation of promoter regions of housekeeping genes leads to gene silencing. Additional epigenetic events, such as histone methylation and acetylation, also play a very important role in the definitive repression of gene expression by DNA methylation. If the aberrant DNA methylation of promoter regions is the starting or the secondary event leading to the gene silencing is still debated. Mechanisms controlling DNA methylation patterns do exist although they have not been ultimately proven. Our data suggest that poly(ADP-ribosyl)ation might be part of this control mechanism. Thus an additional epigenetic modification seems to be involved in maintaining tissue and cell-type methylation patterns that when formed during embryo development, have to be rigorously conserved in adult organisms.Key words: DNA methylation, chromatin, poly(ADP-ribosyl)ation.
Communication over a large distance: enhancers and insulators
Authors: Bondarenko Vladimir A , Liu Ye V , Jiang Yong I , Studitsky Vasily M
Published: July 2003

Enhancers are regulatory DNA sequences that can work over a large distance. Efficient enhancer action over a distance clearly requires special mechanisms for facilitating communication between the enhancer and its target. While the chromatin looping model can explain the majority of the observations, some recent experimental findings suggest that a chromatin scanning mechanism is used to establish the loop. These new findings help to understand the mechanism of action of the elements that can prevent enhancerpromoter communication (insulators).Key words: enhancers, transcription activation, chromatin, insulators.
The many roles of the transcriptional regulator CTCF
Authors: Dunn Katherine L , Davie James R
Published: July 2003

The nuclear factor CTCF was first identified as one of the factors binding to the regulatory regions of the c-myc gene. Further study of this protein revealed roles in transcriptional repression, insulator function, and imprinting genetic information. Recent studies have provided new insight into the mechanism through which this factor acts at various levels of gene regulation.Key words: CTCF, insulator, transcription.
Sperm chromatin remodelling andWolbachia-induced cytoplasmic incompatibility inDrosophila
Authors: Harris Harriet L , Braig Henk R
Published: July 2003

Wolbachia pipientis is an obligate bacterial endosymbiont, which has successfully invaded approximately 20% of all insect species by manipulating their normal developmental patterns. Wolbachia-induced phenotypes include parthenogenesis, male killing, and, most notably, cytoplasmic incompatibility. In the future these phenotypes might be useful in controlling or modifying insect populations but this will depend on our understanding of the basic molecular processes underlying insect fertilization and development. Wolbachia-infected Drosophila simulans express high levels of cytoplasmic incompatibility in which the sperm nucleus is modified and does not form a normal male pronucleus when fertilizing eggs from uninfected females. The sperm modification is somehow rescued in eggs infected with the same strain of Wolbachia. Thus, D. simulans has become an excellent model organism for investigating the manner in which endosymbionts can alter reproductive programs in insect hosts. This paper reviews the current knowledge of Drosophila early development and particularly sperm function. Developmental mutations in Drosophila that are known to affect sperm function will also be discussed.Key words: sperm chromatin, fertilization, Drosophila, Wolbachia, cytoplasmic incompatibility.
Tubulyzine®, a novel tri-substituted triazine, prevents the early cell death of transplanted myogenic cells and improves transplantation success
Authors: Fahime E El , Bouchentouf M , Benabdallah B F , Skuk D , Lafreniere J F , Chang Y T , Tremblay J P
Published: July 2003

Myoblast transplantation (MT) is a potential therapeutic approach for several muscular dystrophies. A major limiting factor is that only a low percentage of the transplanted myoblasts survives the procedure. Recent advances regarding how and when the myoblasts die indicate that events preceding actual tissue implantation and during the first days after the transplantation are crucial. Myoseverin, a recently identified tri-substituted purine, was shown to induce in vitro the fission of multinucleated myotubes and affect the expression of a variety of growth factors, and immunomodulation, extracellular matrix-remodeling, and stress response genes. Since the effects of myoseverin are consistent with the activation of pathways involved in wound healing and tissue regeneration, we have investigated whether pretreatment and co-injection of myoblasts with Tubulyzine®(microtubule lysing triazine), an optimized myoseverin-like molecule recently identified from a triazine library, could reduce myoblast cell death following their transplantation and consequently improves the success of myoblast transplantation. In vitro, using annexin-V labeling, we showed that Tubulyzine (5 µM) prevents normal myoblasts from apoptosis induced by staurosporine (1 µM). In vivo, the pretreatment and co-injection of immortal and normal myoblasts with Tubulyzine reduced significantly cell death (assessed by the radio-labeled thymidine of donor DNA) and increased survival of myoblasts transplanted in Tibialis anterior (TA) muscles of mdx mice, thus giving rise to more hybrid myofibers compared to transplanted untreated cells. Our results suggest that Tubulyzine can be used as an in vivo survival factor to improve the myoblast-mediated gene transfer approach.Key words: myoblast survival, mdx mouse, myoblast transplantation, microtubule-binding molecule, cell death.
Singlet-oxygen reactions sensitized on solid surfaces of lignin or titanium dioxide: Product studies from hindered secondary amines and from lipid peroxidation
Authors: Barclay L RC , Basque M -C , Vinqvist M R
Published: July 2003

Product analyses and kinetic methods were used to determine the role of singlet oxygen in lignin-catalyzed oxidations of organic substrates. Method A used the ESR analysis of nitroxide radicals formed by singlet oxygen (Type II) on 2,2,6,6-tetramethylpiperidine, 1, or tetramethylpiperidone, 2. Method B used HPLC analysis of the 9- and 13-linoleate chain hydroperoxides formed on oxidation of methyl linoleate to distinguish free-radical peroxidation (Type I) from singlet-oxygen oxidation (Type II) on the basis of different cis,trans (kinetic) to trans,trans (thermodynamic) product ratios. Applications of method A to solid dispersions of lignin or titanium dioxide (TiO2, a known singlet-oxygen sensitizer) indicated singlet-oxygen reactions. In addition to the nitroxide triplet, irradiation of lignin produces a persistent broad signal in the solid attributed to phenoxyl radicals. Benzophenone and 3,5-di-tert-butyl-ortho-benzoquinone, 5, coated on silica gel were used as models to compare the effects of irradiating such compounds on the products and kinetics of methyl linoleate oxidation. Benzophenone acted as an initiator, giving free-radical peroxidation, whereas 5 or lignin coated with methyl linoleate acted as singlet-oxygen sensitizers, according to both product studies (method B) and the kinetic order in oxygen consumption during UV photolysis. Photolysis of phase-separated sensitizer (TiO2or lignin) and substrate (methyl linoleate) resulted in typical singlet-oxygen products. These results indicate that singlet oxygen plays a significant role in the photo-yellowing of high-lignin-content wood pulps. Key words: lignin, singlet oxygen, mechanism, peroxidation, products.
Intramolecular reactions of dialkoxycarbenes with a carbonyl group
Authors: Dawid Malgorzata , Warkentin John
Published: July 2003

Thermolysis of 5,5-dimethyl-2-methoxy-2-(2-oxocyclohexylmethoxy)-Δ3-1,3,4-oxadiazoline (3a) in benzene at 110°C generated a carbonyl ylide intermediate that gave, in a minor side reaction, a product of 1,3-dipolar cycloaddition to the carbonyl group. The major fate of the ylide was fragmentation to acetone and a dialkoxycarbene, MeO (RCH2O)C:, where R = 2-oxocyclohexyl. The carbene, in turn, underwent overall [2 + 1] cycloaddition to the carbonyl group, presumably to afford diastereomeric dialkoxyoxiranes that could not be isolated. A product of methanolysis of the presumed oxiranes was isolated by GC and its structure was determined by means of X-ray diffraction. Methanol is believed to result from reaction of an intermediate or product with adventitious water. Deliberate hydrolysis of the product of methanolysis gave a hydroxy lactone, the structure of which was also secured by means of single crystal X-ray diffraction. Those structures indicated the likely structures of the oxirane precursors. A second, and major, product from the carbene was a bicyclic ketone. Similar products were obtained from intramolecular reactions of a carbene tethered to cyclopentanone through a two-carbon or a one-carbon tether. Some compounds that are apparently "dimers" of the oxiranes were also isolated and identified by means of X-ray diffraction. These dimers are thought to originate from the reaction of a ring-opened oxirane (a dipole or a cation from electrophilic opening of the oxirane) with a molecule of the oxirane rather than from bimolecular reaction between two oxirane molecules. The oxiranes open by cleavage of the (RO)2CO bond rather than the oxirane CC bond, the normally observed sense of thermal ring opening. The properties of the carbenes and the presumed oxiranes serve to point out the options available to such intermediates and suggest that some new, synthetically useful reactions may become possible.Key words: bicyclic ketone, dialkoxycarbene, dialkoxyoxirane, hydroxylactone, "oxirane dimers".
Alkoxy radicals in the gaseous phase: β-scission reactions and formation by radical addition to carbonyl compounds
Authors: Rauk Arvi , Boyd Russell J , Boyd Susan L , Henry David J , Radom Leo
Published: July 2003

The structures and reactivities of the alkoxy radicals methoxy (CH3O·), ethoxy (CH3CH2O·), 1-propoxy (CH3CH2CH2O·), 2-propoxy ((CH3)2CHO·), 2-butoxy (CH3CH2CH(CH3)O·), tert-butoxy ((CH3)3CO·), prop-2-enoxy (CH2=CHCH2O·), and but-3-en-2-oxy (CH2=CHCH(CH3)O·) have been investigated at the B3-LYP/6-31G(d) and CBS-RAD levels of theory. Enthalpies of formation (ΔfH°298) were calculated with CBS-RAD for all the alkoxy radicals, the carbonyl and radical products of β-scission reactions, and the transition structures leading to them. The mean absolute deviation between the predicted and available experimental ΔfH°298 values is 5.4 kJ mol1. Eyring (ΔH0, ΔH298, ΔG298) and Arrhenius (log A, Ea) activation parameters for both the forward (β-scission) and reverse (radical addition to carbonyl) pathways were calculated. Agreement with available experimental data is very good, generally within 15 kJ mol1 for Ea, and 0.5 for log A. The transition structures are found to be substantially polarized, with the departing radical slightly positive, the O atom negative, and the rest of the molecule positive. The barriers for the β-scission reactions decrease with decreasing endothermicity and with decreasing ionization energy of the departing radical.Key words: alkoxy, alkoxyl, radical, addition, carbonyl, β-scission, calculaton, electronic structure, B3LYP, CBS-RAD, thermochemistry.
Stereospecific Grignard reactions of cholesteryl 1-alkenesulfinate esters: Application of the Andersen Protocol to the preparation of non-racemic α,β-unsaturated sulfoxides
Authors: Strickler Rick R , Motto John M , Humber Craig C , Schwan Adrian L
Published: July 2003

Enantiomerically enriched α,β-unsaturated sulfinate esters of ()-cholesterol undergo stereospecific substitutions at sulfur when treated in benzene at 6°C with Grignard reagents. Sulfoxides with ees of 8599.5% are obtained when enantiopure sulfinates are used. The substitution reactions proceed with inversion of sulfur configuration. Enantiomerically pure cholesteryl (E)-2-carbomethoxyethenesulfinate is not a suitable reactant under the Grignard reaction conditions. It is suggested that the ester group induces unwanted reactions significantly lowering both the yield and sulfur stereogenicity.Key words: sulfinate, sulfoxide, Grignard reagents, stereospecific, unsaturated.