Extracellular vesicles: exosomes,microparticles, their parts,and their targets to enable their biomanufacturing and clinical applications

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Chromosome bands, their chromatin flavors, and their functional features.

To show that the input pattern of chromosomal mutations is highly organized relative to the band patterns along human chromosomes, a new term, "metaphase chromatin flavor," is introduced. Five different flavors of euchromatic metaphase bands are cytologically identified along a human ideogram. These are G-bands and, based upon combinations of extreme Alu richness and GC richness, four different R-band flavors. The two flavors with extremely GC-rich components, traditionally called "T-bands," represent only 15% of all bands. However, they contain 65% of mapped genes, 19 of 25 mapped oncogenes, most cancer-associated rearrangements, evolutionary rearrangements, meiotic chiasmata, and X-ray-induced breaks. Flavors with extremely Alu-rich flavors are also involved in melphalan-induced rearrangements, pachytene stretching, and mitotic chiasmata. Frequencies of CpG islands, CCGCCC boxes, retroposon families, and genes are characteristic to each chromatin flavor and will facilitate alignment of genome sequences onto ideograms of chromatin flavor. The influence of chromatin flavor on the evolution of a gene's sequence is so strong that one can infer the flavor of the band in which a gene resides from the sequence of the gene itself. Correlation coefficients for many pairs of mapped genetic variables, while globally high, are quite low within bands of one flavor, implicating a concerted mode of evolution for bands of one chromatin flavor.     

Dinoflagellates,diatoms, and their viruses

Since the first discovery of the very high virus abundance in marine environments, a number of researchers were fascinated with the world of "marine viruses", which had previously been mostly overlooked in studies on marine ecosystems. In the present paper, the possible role of viruses infecting marine eukaryotic microalgae is enlightened, especially summarizing the most up-to-the-minute information of marine viruses infecting bloom-forming dinoflagellates and diatoms. To author's knowledge, approximately 40 viruses infecting marine eukaryotic algae have been isolated and characterized to different extents. Among them, a double-stranded DNA (dsDNA) virus "HcV" and a single-stranded RNA (ssRNA) virus "HcRNAV" are the only dinoflagellate-infecting (lytic) viruses that were made into culture; their hosts are a bivalve-killing dinoflagellate Heterocapsa circularisquama. In this article, ecological relationship between H. circularisquama and its viruses is focused. On the other hand, several diatom-infecting viruses were recently isolated and partially characterized; among them, one is infectious to a pen-shaped bloom-forming diatom species Rhizosolenia setigera; some viruses are infectious to genus Chaetoceros which is one of the most abundant and diverse diatom group. Although the ecological relationships between diatoms and their viruses have not been sufficiently elucidated, viral infection is considered to be one of the significant factors affecting dynamics of diatoms in nature. Besides, both the dinoflagellate-infecting viruses and diatom-infecting viruses are so unique from the viewpoint of virus taxonomy; they are remarkably different from any other viruses ever reported. Studies on these viruses lead to an idea that ocean may be a treasury of novel viruses equipped with fascinating functions and ecological roles.     

Ethnobotany of Tokelau: The plants,their Tokelau names,and their uses

Three research trips were made to the Tokelau Islands (including Swains Island), located north of Samoa in Western Polynesia, and a collection of the flora of the islands was made. At the same time, Tokelauan informants were interviewed about native names and uses of plants found there. This information was augmented by a literature review, by data on plant specimens stored at the Bernice P. Bishop Museum, and by interviews with other Tokelauans now living in Samoa. From this information, an account of Tokelauan plant names and their ethnobotanical uses was compiled.     

Words,antibodies and their interactions

Jerne’s idiotypic network theory stresses the importance of antibody-to-antibody interactions and provides possible explanations for self-tolerance and increased diversity in the immune repertoire. In this paper, we use an immune network model to build a user profile for adaptive information filtering. Antibody-to-antibody interactions in the profile’s network model correlations between words in text. The user profile has to be able to represent a user’s multiple interests and adapt to changes in them over time. This is a complex and dynamic engineering problem with clear analogies to the immune process of self-assertion. We present a series of experiments investigating the effect of term correlations on the user’s profile performance. The results show that term correlations can encode additional information, which has a positive effect on the profile’s ability to assess the relevance of documents to the user’s interests and to adapt to changes in them.     

Morphogens, their identification and regulation

During the course of development, cells of many tissues differentiate according to the positional information that is set by the concentration gradients of morphogens. Morphogens are signaling molecules that emanate from a restricted region of a tissue and spread away from their source to form a concentration gradient. As the fate of each cell in the field depends on the concentration of the morphogen signal, the gradient prefigures the pattern of development. In this article, we describe how morphogens and their functions have been identified and analyzed, focusing on model systems that have been extensively studied.     

Sufficient-completeness, ground-reducibility and their complexity

Summary The sufficient-completeness property of equational algebraic specifications has been found useful in providing guidelines for designing abstract data type specifications as well as in proving inductive properties using the induction-less-induction method. The sufficient-completeness property is known to be undecidable in general. In an earlier paper, it was shown to be decidable for constructor-preserving, complete (canonical) term rewriting systems, even when there are relations among constructor symbols. In this paper, the complexity of the sufficient-completeness property is analyzed for different classes of term rewriting systems. A number of results about the complexity of the sufficient-completeness property for complete (canonical) term rewriting systems are proved: (i) The problem is co-NP-complete for term rewriting systems with free constructors (i.e., no relations among constructors are allowed), (ii) the problem remains co-NP-complete for term rewriting systems with unary and nullary constructors, even when there are relations among constructors, (iii) the problem is provably in almost exponential time for left-linear term rewriting systems with relations among constructors, and (iv) for left-linear complete constructor-preserving rewriting systems, the problem can be decided in steps exponential innlogn wheren is the size of the rewriting system. No better lower-bound for the complexity of the sufficient-completeness property for complete (canonical) term rewriting system with nonlinear left-hand sides is known. An algorithm for left-linear complete constructor-preserving rewriting systems is also discussed. Finally, the sufficient-completeness property is shown to be undecidable for non-linear complete term rewriting systems with associative functions. These complexity results also apply to the ground-reducibility property (also called inductive-reducibility) which is known to be directly related to the sufficient-completeness property.Some of the results in this paper were reported in a paper titled Complexity of Sufficient-Completeness presented at theSixth Conf. on Foundations of Software Technology and Theoretical Computer Science, New Delhi, India, Dec. 1986. The term quasi-reducibility is replaced in this paper by ground-reducibility as the latter seems to convey a lot more about the concept than the former.Partially supported by the National Science Foundation Grant nos. CCR-8408461 and CCR-8906678Partially supported by the National Science Foundation Grant nos. CCR-8408461 and CCR-9009414Partially supported by the National Science Foundation Grant no. DCR-8603184     

Lincomycin,clindamycin and their applications

Lincomycin and clindamycin are lincosamide antibiotics used in clinical practice. Both antibiotics are bacteriostatic and inhibit protein synthesis in sensitive bacteria. They may even be bactericidal at the higher concentrations that can be reached in vivo . Clindamycin is usually more active than lincomycin in the treatment of bacterial infections, in particular those caused by anaerobic species; and it can also be used for the treatment of important protozoal diseases, e.g. malaria, most effectively in combination with primaquine. Resistance to lincomycin and clindamycin may be caused by methylation of 23S ribosomal RNA, modification of the antibiotics by specific enzymes or active efflux from the periplasmic space.     

Space bioreactors: their use,their future

The use of bioreactors during space flight is discussed. The major elements of a bioreactor are a culture chamber, sensors, a control unit with feedback, as gas exchange system, a pump, fresh culture medium, and a waste reservoir. Types of bioreactors developed for use in space include the Woodlawn Wanderer 9 apparatus, the Space tissue loss system, rotating wall vessel, dynamic cell culture system and the SBR I. Future development for space bioreactors include improvements for cultivation of mammalian cells and tissue engineering and the transfer of bioreactor technology for earth-bound instruments.     

Relationships among microarthropods,fungi, and their environment

Temporal and spatial relationships in a maple-forest soil among mycophagous microarthropods, total hyphal length, vesicular-arbuscular mycorrhizal (VAM) fungus spores, microfungus diversity, root biomass and some abiotic variables (temperature, water content, pH, organic matter content) were investigated. Samples were obtained from spring 1991 to winter 1992 at four soil depths. Canonical correspondence analysis was used to analyze the data. Four species of sporulating VAM fungi were identified, along with 23 species of mites and springtails, 9 of which were common. Hyphal length, VAM fungus spores, and soil animals peaked in spring and autumn. Canonical correspondence analysis suggests that animal abundance and success in the soil is dependent on a number of environmental variables. The most important variables that influence microarthropod community structure are: (i) temperature, (ii) water content, (iii) pH, (iv) total length of fungal hyphae, and (v) diversity of darkly-pigmented fungi. However, the relative importance of these variables changes with increasing soil depth. We have also shown a relationship between arthropod populations and their food supply under field conditions, a phenomenon that has been demonstrated previously under controlled laboratory conditions.     

Yeast killer toxins,molecular mechanisms of their action and their applications

Killer toxins secreted by some yeast strains are the proteins that kill sensitive cells of the same or related yeast genera. In recent years, many new yeast species have been found to be able to produce killer toxins against the pathogenic yeasts, especially Candida albicans. Some of the killer toxins have been purified and characterized, and the genes encoding the killer toxins have been cloned and characterized. Many new targets including different components of cell wall, plasma membrane, tRNA, DNA and others in the sensitive cells for the killer toxin action have been identified so that the new molecular mechanisms of action have been elucidated. However, it is still unknown how some of the newly discovered killer toxins kill the sensitive cells. Studies on the killer phenomenon in yeasts have provided valuable insights into a number of fundamental aspects of eukaryotic cell biology and interactions of different eukaryotic cells. Elucidation of the molecular mechanisms of their action will be helpful to develop the strategies to fight more and more harmful yeasts.     

Plants,insects, and man—their interrelationships

Plants constitute a vast cornucopia of chemical substances used for defense from attack by insects. These may be classified as insect attractants, repellents, toxicants, inhibitors of growth and development, sterilants, and feeding deterrents. An overview of the subject and its interrelationships with man is presented.     

Ichthyosauria: their diversity, distribution, and phylogeny

The Ichthyosauria is the group of Mesozoic marine reptiles that was most highly adapted to the aquatic environment. The first ichthyosaurs from the upper Lower Triassic (Spathian) already show a suite of unique characters (very large eyes, elongate snout, deeply amphicoelous vertebrae, limb modified to fins) correlated with a fully aquatic existence and probably were unable to leave the water. The key evolutionary innovation was vivipary, giving birth to live young, which is documented by the fossil record since the end of the Anisian. Major evolutionary trends in the locomotor apparatus are the increasing modification of the fin skeleton to a mosaic of bones and the change from anguiliform swimming in the earliest forms to thunniform swimming in the Jurassic and later forms, as evidenced by the shortening of the body and the evolution of a semilunate tail fin. Almost from the beginning, ichthyosaurs had a cosmopolitan distribution which was retained until their extinction in the Cenomanian. Ichthyosaurian diversity is greatest in the Middle Triassic with piscivorous, heterodont, and durophagous forms. Jurassic diversity is greatest in the Liassic, declining to one genus (Platypterygius) in the Cretaceous. Although skull characters indicate that ichthyosaurs were diapsids, their exact position within Diapsida is unclear. A cladistic analysis of the well known genera clarifies relationships within the Ichthyosauria. Most basal areGrippia andUtatsusaurus, followed by the Mixosauridae (Mixosaurus andPhalarodon). The Shastasauridae (Cymbospondylus, Shonisaurus, Besanosaurus) are the most advanced Triassic forms and represent the sistergroup of all post-Triassic ichthyosaurs. These are clearly monophyletic and are termed here the Neoichthyosauria.     

Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display

Background  

Depending on chemical features residues have preferred locations – interior or exterior – in protein structures, which also determine how many other residues are found around them. The close packing of residues is the hallmark of protein interior and protein-protein interaction sites.