Evolutionary stable strategy: a test for theories of retroviral pathology which are based upon the concept of molecular mimicry

The genetic makeup of animal and plant populations is determined by established principles and concepts. Ecology and evolution provide a basic theoretical framework for understanding how genetic changes occur in populations. Whether these rules can be applied to host retroviral populations is unknown. Individuals infected with the human immunodeficiency virus (HIV) contain within their bodies a viral population. This population is known as a viral quasispecies. Located in the transmembrane protein of HIV-1 is the viral sequence Gly-Thr-Asp-Arg-Val. Previous immunological studies have shown that viral antibody is produced in response to this five-amino-acid sequence. Antibody to this viral sequence also crossreacts and binds to a related peptide sequence found on certain immune cells. This related sequence, Gly-Thr-Glu-Arg-Val, is found on immune cells bearing a structure known as the major histocompatibility complex (MHC). The viral transmembrane sequence, Gly-Thr-Asp-Arg-Val, can be substituted with alanine residues utilizing site-directed mutagenesis. This creates a viral clone devoid of the genetic similarity with the MHC. Chimpanzees progressing to AIDS contain both sequences of interest. Suppression of the chimpanzee quasispecies utilizing anti-retroviral drugs is proposed. This action serves to suppress the presence of the viruses containing the sequence Gly-Thr-Asp-Arg-Val. When viral load has been reduced significantly, a drug resistant, alanine altered clone is to be introduced in large numbers. The concept of evolutionary stable strategy predicts that a viable HIV clone with alanine residues can genetically dominate the viral population. Immune system recognition of the alanine sequence is likely to result in renewed antibody production. Antibodies to the alanine containing viral sequence should not recognize or bind to the MHC. Immunological parameters can then be measured to determine the physiological impact of eliminating a sequence responsible for molecular mimicry between virus and host.     

A new species of Cudonia based on morphological and molecular data

A discomycete collected in western Sichuan, China, is morphologically intermediate between Cudonia and Spathularia. The fungus has a bright yellow capitate ascigerous head, a white, ridged stalk, and a well-developed membrane covering the whole ascoma. The asci, ascospores, and paraphyses are similar to those of Cudonia and Spathularia. Based on morphology and DNA sequence analysis, a new species, Cudonia sichuanensis, is reported. Cudonia and Spathularia are closely related to members of Rhytismataceae, as has been suggested previously. The similarity of ascoma and ascospore development between these two genera and Lophodermium (Rhytismataceae) is discussed.     

A blueprint for kinetochores - new insights into the molecular mechanics of cell division

Kinetochores are large proteinaceous complexes that physically link centromeric DNA to the plus ends of spindle microtubules. Stable kinetochore-microtubule attachments are a prerequisite for the accurate and efficient distribution of genetic material over multiple generations. In the past decade, concerted research has resulted in the identification of the individual kinetochore building blocks, the characterization of critical microtubule-interacting components, such as the NDC80 complex, and the development of an approximate model of the architecture of this sophisticated biological machine.     

Efficient shoot formation on internodal segments and alkaloid formation in the regenerates of Cephaelis ipecacuanha A. Richard

Rapid shoot proliferation was established by adventitious shoot formation on internodal segments. Cross sections of the shoot initiation area were observed microscopically and adventitious shoots were studied under the scanning electron microscope. Shoots were directly formed on the epidermis of internodal segments in vitro without callusing, but not on that of nodal segments with axillary buds. The use of media containing 0.01 – 0.1 mg/l 6-benzyladenine or 0.1 mg /l kinetin and culture under 16 h light increased the number of shoots per segment. The shoots thus obtained were rooted on phytohormone-free Woody Plant or Gamborg B5 solid medium, and were then transferred to soil. When potted, these grew well in a greenhouse. The emetic alkaloid content of adventitious shoots and regenerated plants was determined by HPLC. In vitro shoots cultured in Woody Plant liquid medium supplemented with 0.01 – 0.1 mg/l 6-benzyladenine contained 0.04 – 0.07 % dry wt. emetine and 0.4 – 0.5 % dry wt. cephaeline. One-year old regenerated plants cultivated in a greenhouse demonstrated the same alkaloid content (roots contained 0.82 % dry wt. emetine and 2.16 % dry wt. cephaeline) as the parental plant.Abbreviations MS Murashige — Skoog (Murashige and Skoog 1962) - 1/2 MS half strength MS - B5 Gamborg B5 (Gamborg et al. 1968)] - WP woody plant (Lloyd and McCown 1980) - RC root culture (Thomas and Davey 1982) - HF phytohormone free - BA 6-benzyladenine - Kin kinetin - SEM scanning electron microscopy - RDF rotating drum fermenter     

A molecular orbital study of stability and the conformation of double-stranded DNA-like polymers

The stacking and hydrogen bonding energies between bases in the B form of DNA were calculated by a perturbation method using the wave functions by the CNDO and the P-P-P methods. The exchange energies were calculated by using the corresponding orbitals. The magnitudes of the sums of the average stacking and hydrogen bonding energies per base pair of double-stranded DNA-like polymers are in good parallel with the melting temperatures of the polymers. The polymers containing I-C pairs are exceptions to this relation. Intrastrand stacking bases have the potential minimum at the distances of 2·8–3·7 Å. The minimum of stacking energy of double-stranded polymer for rotation of base pair around the helix axis exists near 36°. The deviation of the potential minimum from 36° seems to parallel the feature of the X-ray diffraction pattern of the polymer.     

A new concept in the molecular process of muscle contraction: functional role of phosphorylated amino acids in myosin

In this report a summary is given of our experiments concerning the in vivo endogenous phosphate (P) content of myosin. It was found that besides the ester type phosphates of myosin there was a considerable amount of N-P type energy-rich phosphoryl groups bond to the basic amino acids of peptide chains. The endogenous P concentration of myosin depends on the source of the preparation. The concentration of P is much higher in myosin preparations of well-trained animals and human subjects compared to those found in the control muscles. As the P binding sites of fresh purified myosin are only partially saturated, the preparations can incorporate P up to a definite saturation only. The phosphorylating ability of myosins disappears after prolonged storage as a consequence of an alteration in structure of the myosin molecule. The P groups are moving inside the myosin molecule. It is supposed that the inorganic P release promoted by actin is connected with the thin filament movements towards the centre of the sarcomere, furthermore P replenishment, P linking and movement involve N3-trimethyl-lysine, 3-methylhistidine, P-Arg and two conformers of P-His. The two net negative charges of P group form electric monopoles of a minor battery (myosin head). They help to force generation at head rotation (90 degrees-45 degrees angle) and produce free energy changes that can be calculated from the number of N-P bonds.     

A molecular model for the formation and properties of fluid gels

The effects of biopolymer gelation in a shear field are discussed. Gel particles are produced if the gelation mechanism involves an aggregation step. Particular attention is paid to the molecular events of ordering and aggregation upon cooling, investigating the differences in such processes as a result of shearing during gelation. A model is proposed which follows the conception of the particles, their growth, physical properties and stability.     

A new classification of the long-horned caddisflies (Trichoptera: Leptoceridae) based on molecular data

Background  

Leptoceridae are among the three largest families of Trichoptera (caddisflies). The current classification is founded on a phylogenetic work from the 1980's, based on morphological characters from adult males, i.e. wing venation, tibial spur formula and genital morphology. In order to get a new opinion about the relationships within the family, we undertook a molecular study of the family based on sequences from five genes, mitochondrial COI and the four nuclear genes CAD, EF-1α, IDH and POL.     

A new concept of olfactory biosensor based on interdigitated microelectrodes and immobilized yeasts expressing the human receptor OR17-40

This work shows the feasibility of an olfactory biosensor based on the immobilization of Saccharomyces cerevisiae yeast cells genetically modified to express the human olfactory receptor OR17-40 onto interdigitated microconductometric electrodes. This olfactory biosensor has been applied to the detection of its specific odorant (helional) with a high sensitivity (threshold 10⁻¹⁴ M). In contrast, no significant response was observed using a non-specific odorant (heptanal), which suggests a good selectivity. Thus, this work may represent a first step towards a new kind of bioelectronic noses based on whole yeast cells and allowing a real time monitoring of olfactory receptor activation. Presented at the joint biannual meeting of the SFB-GEIMM-GRIP, Anglet, France, 14–19 October, 2006.     

Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function.

Solutions to the nonlinear Poisson-Boltzmann equation were used to obtain the electrostatic potentials of RNA molecules that have known three-dimensional structures. The results are described in terms of isopotential contours and surface electrostatic potential maps. Both representations have unexpected features: 'cavities' within isopotential contours and areas of enhanced negative potential on molecular surfaces. Intriguingly, the sites of unusual electrostatic features correspond to functionally important regions, suggesting that electrostatic properties play a key role in RNA recognition and stabilization. These calculations reveal that the electrostatic potentials generated by RNA molecules have a variety of functionally important characteristics that cannot be discerned by simple visual inspection of the molecular structure.     

A new electron transport mechanism in mitochondrial steroid hydroxylase systems based on structural changes upon the reduction of adrenodoxin

The adrenal ferredoxin (adrenodoxin, Adx) is an acidic 14.4-kDa [2Fe-2S] ferredoxin that belongs to the vertebrate ferredoxin family. It is involved in the electron transfer from the flavoenzyme NADPH-adrenodoxin-reductase to cytochromes P-450(scc) and P-450(11)(beta). The interaction between the redox partners during electron transport has not yet been fully established. Determining the tertiary structure of an electron-transfer protein may be very helpful in understanding the transport mechanism. In the present work, we report a structural study on the oxidized and reduced forms of bovine adrenodoxin (bAdx) in solution using high-resolution NMR spectroscopy. The protein was produced in Escherichia coli and singly or doubly labeled with (15)N or (13)C/(15)N, respectively. Approximately 70 and 75% of the (15)N, (13)C, and (1)H resonances could be assigned for the reduced and the oxidized bAdx, respectively. The secondary and tertiary structures of the reduced and oxidized states were determined using NOE distance information. (1)H(N)-T(1) relaxation times of certain residues were used to obtain additional distance constraints to the [2Fe-2S] cluster. The results suggest that the solution structure of oxidized Adx is quite similar to the X-ray structure. However, structural changes occur upon reduction of the [2Fe-2S] cluster, as indicated by NMR measurements. It could be shown that these conformational changes, especially in the C-terminal region, cause the dissociation of the Adx dimer upon reduction. A new electron transport mechanism proceeding via a modified shuttle mechanism, with both monomers and dimers acting as electron carriers, is proposed.     

Chemical modification of wheat-protein-based natural polymers: formation of polymer networks with alkoxysilanes to modify molecular motions and enhance the material performance

The mechanical performance of plasticized wheat gluten (WG) materials was significantly modified through the formation of different chemical and network structures with alkoxysilanes. The epoxy-functionalized alkoxysilanes were grafted to segments of WG, and then the condensation reactions between alkoxysilane segments occurred during thermal processing to form WG-siloxane networks. The mechanical properties and molecular motions of the networks were dependent on the amount and type of alkoxysilanes applied. A lower amount of alkoxysilanes caused the alkoxysilane molecules to predominately graft onto WG chains without forming linkages between WG segments, which produced an additional plasticizing effect on the WG systems with a longer elongation value and weaker tensile strength at relative humidity (RH) = 50% as compared to the WG system. However, such grafting improved the hydrostability of the materials and generated an improvement in tensile strength at RH = 85%. Increasing the amount of alkoxysilanes in the systems led to the formation of cross-linked WG-siloxane networks via linkages between alkoxysilane segments. Remarkable strength improvement was obtained for the networks with elongation values still higher than the original plasticized WG due to the flexible nature of the siloxane components. A more significant strength improvement was obtained for the WG-SiA systems at both RH = 50% and 85%, where SiA could form three-dimensional networks from siloxane condensation and generate highly cross-linked network structures with relatively low mobility. For WG-SiB systems, SiB could only form linear linkages, and the higher mobility of the SiB phase caused the systems to display a lower strength improvement with a longer elongation value.     

Relationships and taxonomic status of Alternaria radicina, A. carotiincultae, and A. petroselini based upon morphological, biochemical, and molecular characteristics

Alternaria radicina, A. carotiincultae, and A. petroselini are closely related pathogens of umbelliferous crops. Relationships among these fungi were determined based on growth rate, spore morphology, cultural characteristics, toxin production, and host range. Random amplified polymorphic DNA (RAPD) analysis of these species, other species of Alternaria, and closely related fungi was also performed. A. petroselini was readily differentiated from A. radicina and A. carotiincultae on the basis of spore morphology, production of microsclerotia, host range, and RAPD analysis. Alternaria radicina and A. carotiincultae were considerably more similar to each other than to A. petroselini, but could be differentiated on the basis of growth rate, spore morphology, colony morphology, and, to a limited extent, RAPD analysis. When grown on media having a high nutritional content, A. radicina produced a diffusible yellow pigment and crystals of the fungal metabolite radicinin. In contrast, A. carotiincultae produced little or no radicinin. However, when A. carotiincultae was grown on the same medium amended with radicinin, growth rate and colony and conidial morphology were more similar to those of A. radicina. These results suggest that the morphological differences between A. radicina and A. carotiincultae are due, at least in part, to radicinin production, and that these fungi are conspecific. Therefore, we propose that A. carotiincultae be considered a synonym of A. radicina.     

A strategy for the covalent functionalization of resorbable polymers with heparin and osteoinductive growth factor

The chemical strategy presented herein is the nondestructive preparation of resorbable polymer scaffolds with heparin covalently bonded to the surface and an osteoinductive growth factor, recombinant human bone morphogenetic protein-2, immobilized in the heparin layer. The coupling scheme involves functionalization of surfaces by grafting in the vapor phase with poly( l-lactide) and poly(-caprolactone) films chosen as representative substrates. The biocompatibility of functionalized surfaces was verified by a much improved attachment and proliferation of mesenchymal stem cells (MSC).