Essential degrees of freedom of proteins

Analysis of extended molecular dynamics (MD) simulations of several proteins in aquous solutions reveals that it is possible to separate the configurational space into two subspaces: (1) an essential subspace containing only a few degrees of freedom in which anharmonic motion occurs that comprises most of the positional fluctuations; and (2) the remaining space in which the motion has a narrow Gaussian distribution and which can be considered as physically constrained.     

Modulation of natural killer activity by thymosin alpha 1 and interferon

Summary A single injection of -interferon (-IFN) (30 000 units/mouse), a major biological modifier of natural killer (NK) cytolytic activity, strongly stimulated NK activity in normal mice, as expected, while the same treatment did not statistically alter the NK response in cyclophosphamide (CY)-suppressed animals.We investigated the possibility of thymosin ₁ cooperating with -IFN in boosting NK activity in CY-suppressed animals.The results show that treatment with thymosin ₁ (200 g/kg) for 4 days, followed by a single injection of -IFN 24 h before testing, strongly restored NK activity in CY-suppressed mice. Thymosin ₁ was, moreover, able to accelerate the recovery rate of NK activity in bone marrow reconstituted murine chimeras.Taken together the data support the concept that the synergic effect between thymosin ₁ and -IFN could be the result of effects on differentiation of the NK lineage at different levels.     

Cluster Maintenance in Mobile Ad-hoc Networks

The main contribution of this paper is to propose a new cluster maintenance algorithm and a companion cluster initialization algorithm based on a number of interesting and novel properties of diameter-2 graphs. The initialization algorithm naturally blends into cluster maintenance, showing the unity between these two operations. We refer to our algorithms as tree-based since they depend on a spanning tree maintained at various nodes. Unlike the vast majority of published clustering algorithms, our algorithms are cluster-centric, as opposed to node-centric, and work in the presence of node mobility. Extensive simulation results have shown the effectiveness of our algorithms when compared to other clustering schemes proposed in the literature.Lan Wang received his B.S. and M.S. degrees in computer science from Harbin Engineering University, China in 1992 and 1995, respectively. From 1995 to 1999, he worked as a software engineer at the System Engineering Research Institute of CSSC, Beijing, China. He is currently a PhD student at the Computer Science Department of Old Dominion University.Stephan Olariu received the M.Sc. and Ph.D. degrees in computer science from McGill University, Montreal, Canada in 1983 and 1986, respectively. In 1986 he joined the Computer Science Department at Old Dominion University where he is now a full professor. He has published extensively in various journals, book chapters, and conference proceedings. His research interests include wireless networks and mobile computing, parallel and distributed systems, performance evaluation, and medical image processing. Prof. Olariu serves on the editorial board of several archival journals including IEEE Transactions on Parallel and Distributed Systems, Journal of Parallel and Distributed Computing, International Journal of Foundations of Computer Science, Journal of Supercomputing, International Journal of Computer Mathematics, VLSI Design, and Parallel Algorithms and Applications.     

Differentiation and redifferentiation of a transfer cell: Development of septal nectaries ofAloe andGasteria

Summary The epithelial cells of the septal nectaries ofGasteria andAloe have a second wall layer consisting of numerous irregular wall protuberances along the outer wall. They, thus, are typical transfer cells. The wall protuberances develop a short time before the nectar secretion begins. At this time and during the secretory phase the amount of microtubules is at a minimum. After the secretion phase the protuberances disappear gradually while often callose is formed between them. Simultaneously a third wall layer is deposited which covers the remnants of the second layer. During the first developmental stages the cells contain amyloplasts with changing amounts of starch. In the redifferentiation phase they become chloroplasts with a crystalline prolamellar body and small stacks of thylakoids.     

Comparison of different strains ofCellulomonas for production of cellulolytic and xylanolytic enzymes from biomass produced on saline lands

A comparison of the rate of carboxymethyl cellulase (CMCase), avicelase, xylanase, -glucosidase and -xylosidase production and rates of growth by 4 different strains ofCellulomonas revealed a wide range of behaviour; with some strains producing more CMCase, avicelase, xylanase, -glucosidase and -xylosidase from complex lignocellulosic (LC) biomass (from saline land) and CMC while some others producing small amounts of these enzymes. One strain,C. biazotea, was better with respect to enzyme production potential and growth behaviour than most of the other strains and has been chosen as a starting strain for genetic improvement for producing enzymes of the cellulase complex.     

Organization of the nervous system of physonectid siphonophores

Summary An antiserum to the sequence Arg-Phe-amide (RFamide) was used to stain the nervous systems of various physonectid siphonophores. In the stem of Nanomia bijuga, this antiserum stained an ectodermal nerve net, which was interrupted, at regular intervals, by transverse collars of neurons. Injection of Lucifer yellow into the giant axon of the stem showed that this axon was dye-coupled to an ectodermal nerve net that resembled the RFamide-positive network. Ectodermal nets of neurons were also found in the pneumatophore, gastrozooids, tentacles and tentilla. At the junctions of the pneumatophore, the gastrozooids, the dactylozooids and the gonozooids with the stem, and at the junctions of tentacles and tentilla, collars or rings of neurons occurred. The stem was connected to the phyllozooids and nectophores by muscular lamellae, which were bordered by chains of neurons. At the margin of the nectophores, an immunoreactive nerve ring was found. Connected to this ring and located in theseitliche Zapfen (sidely-located patche), were two agglomerations of nerve cells. On the upper side of the bell margin, positioned at 90° relative to the seitliche Zapfen, a delta-shaped neuronal structure was found. This structure was connected to the nerve ring and was associated with a muscle, which ran a short distance along the exumbrellar surface.The nervous systems of Agalma elegans, Forskalia edwardsi, Forskalia leuckarti and Halistemma rubrum resembled that of Nanomia bijuga in all major respects.     

Rotational diffusion tensor of nucleic acids from 13C NMR relaxation

Rotational diffusion properties have been derived for the DNA dodecamer d(CGCGAATTCGCG)₂ from ¹³C R₁ and R₁ measurements on the C₁, C₃, and C₄ carbons in samples uniformly enriched in ¹³C. The narrow range of C-H bond vector orientations relative to the DNA axis make the analysis particularly sensitive to small structural deviations. As a result, the R₁/R₁ ratios are found to fit poorly to the crystal structures of this dodecamer, but well to a recent solution NMR structure, determined in liquid crystalline media, even though globally the structures are quite similar. A fit of the R₁/R₁ ratios to the solution structure is optimal for an axially symmetric rotational diffusion model, with a diffusion anisotropy, D_||/D, of 2.1±0.4, and an overall rotational correlation time, (2D_||+4D)^–1, of 3.35 ns at 35 °C in D₂O, in excellent agreement with values obtained from hydrodynamic modeling.     

Structure of root nodules formed by Rhizobium on the non-legume Trema cannabina var. scabra

The structure of the nodules formed by Rhizobium on the non-legume Trema cannabina var. scabra was studied using the light microscope. The overall features of the nodules showed greater resemblance to the non-legume rather than the legume nodule. Nodule squashes yielded bundles of infection threads and bacteroids with morphological differences from rhizobial cells grown on yeast-mannitol-glucose agar. Two types of cell infection occurred within the bacterial zone; plant cells were either, like legumes, filled with rhizobia released from the infection threads (less than one third of infected cells) or were filled with the extensive growth and development of the infection thread. The rate of nitrogen fixation in the Trema nodule was high. It seemed that host cells filled with threads were active in N fixation.     

Biometeorological comfort index

The paper aims to represent and scale biometeorological sensations through a thermal index which comprises the effects of temperature, humidity and wind. The cooling power of a measured combination of wind speed and air temperature is equated with that due to the combination of a reference wind speed (related to the air movement experienced by a person walking in still air), and a derived aerodynamic temperature. A biometeorological temperature which is the average of such an aerodynamic temperature and a conventionally measured wet bulb temperature is shown to afford a better measure of comfort in Spain than some other, alternative indices.     

Immunocytological detection and localization of a peptide reacting with an α-endorphin antiserum in the corticotropic and melanotropic cells of the trout pituitary (Salmo irideus Gibb)

Summary In the pituitary of the trout, the corticotropic and melanotropic cells display a strong immunocytological reaction with -endorphin antiserum. This reaction persists even when a-endorphin antisera treated with -1-24 ACTH or -MSH are used. In the absence of pharmacological tests on the endorphic potencies of the compounds involved in the immunoreaction, it is not yet clear whether this reaction is due to the presence of an -endorphin-like peptide or simply an immunologically related peptide without the properties of endorphin. However, the presence of such peptides in the fish pituitary is interesting from the comparative point of view.     

Helix formation in reduced, S-carboxymethylated human choriogonadotropin beta subunit and tryptic peptides

The subunit of human choriogonadotropin (hCG) and its asialoderivative were digested with trypsin and then reduced and S-carboxymethylated. A series of peptides were purified which corresponded to residues 1–43, 44–95, 96–114, and 123–145 of the 145 amino acid residue glycoprotein. The two N-linked oligosaccharides were present on the amino terminal peptide, and three of the four O-linked oligosaccharides were present on the carboxy terminal peptide. Circular dichroic spectra between 190–240 nm were obtained on reduced, S-carboxymethylated (RCM) hCG and the above peptides, both in aqueous solution and in the helicogenic solvent 80% (vol/vol) trifluoroethanol (TFE). In aqueous solution there was evidence of only limited helicity in the peptides and RCM-hCG however, in the presence of TFE, peptides 1–43 and 44–95 exhibited significant helicity, as did the full-length linear chain. The helicity developed in TFE by RCM-hCG appears much greater than that which occurs in the native, disulfide-intact form, thus suggesting that the disulfides prevent expression of helicity in regions with -helix potential. Application of the Chou-Fasman secondary structure predictive algorithm to hCG suggested that several regions of helix potential, in particular regions 14–21, 59–69, and perhaps 80–88, may account for much of the helicity observed in peptides 1–43 and 44–95, respectively, in TFE. The region from 96–145 has no significant potential for helicity, consistent with the measured circular dichroic spectra of peptides 96–114 and 123–145. These results demonstrate that helicity can occur in the linear form of hCG, and this secondary structure can best be attributed to the amino terminal and the middle portion of the molecule. Several potential regions of -structure and -turns were also suggested.     

Ecological theories and Dutch nature conservation

This paper aims to achieve insight into various ecological theories in the Netherlands which have different, and sometimes opposing, views on the conservation of nature. Interviews, publications and archival research brought to light four separate theories: vitalistic/holistic, dynamic, cybernetic and chaos. Diversity is reached through stability according to vitalistic/holistic and cybernetic theories, but through change and instablility according to the dynamic and chaos theories. These two groups are working apart, and continue to have their own ideas. Prediction of the future is only possible with the vitalistic/holistic and cybernetic theories. Ecologists who adhere to these theories feel responsible and able in different ways to change ecological nature towards desirable end goals. The other two theories, dynamic and chaos, appear to be less activist.     

Morphologische und statistische Untersuchungen an Zellkernen von Ratten und Mäusen zur Frage einer cytologischen Geschlechtsdiagnostik

Zusammenfassung An Blutausstrichen und Gewebsschnitten von männlichen und weiblichen Mäusen und Ratten wurde das Vorkommen von geschlechtsspezifischen morphologischen Kernmerkmalen untersucht. Die Kerne der neutrophilen Granulocyten weisen bei beiden Arten keine an den Kernanhängen erkennbare Geschlechtsdifferenz auf. An den Kernen der Parenchymzellen wurde für weibliche und auch für männliche Tiere ein positiver Geschlechtsnachweis auf Grund einer charakteristischen Chromatinverteilung geführt.Wir stimmen dem Vorschlag von Th. Lüers (1957) zu, die Begriffe Geschlechts-bestimmung und Geschlechtsdifferenzierung nur in ihrer ursprünglichen Bedeutung zu verwenden.     

Enzyme formation,cellular breakdown and the distribution of gibberellins in the endosperm of barley

Summary The -amylase contents of the dorsal and ventral sides of the endosperm of barley grains increase approximately equally during germination. Aleurone tissue from all locations in the grain is equally able to make -amylase in response to gibberellic acid, so the distribution of this enzyme reflects the distribution of endogenous gibberellins.Variations occurred in both the rate and pattern of cellular breakdown of the starchy endosperm. Generally breakdown progressed away from, and parallel to the scutellum, ultimately advancing faster adjacent to the aleurone layer. The sheaf cells, above the furrow, were relatively resistant to enzymic breakdown. The results indicate that gibberellins are released generally from the scutellum and induce hydrolytic enzymes equally on the dorsal and ventral sides of the grain.     

Charles Darwin's theory of evolution: A review of our present understanding

The paper characterizes Darwin's theory, providing a synthesis of recent historical investigations in this area. Darwin's reading of Malthus led him to appreciate the importance of population pressures, and subsequently of natural selection, with the help of the wedge metaphor. But, in itself, natural selection did not furnish an adequate account of the origin of species, for which a principle of divergence was needed. Initially, Darwin attributed this to geographical isolation, but later, following his work on barnacles which underscored the significance of variation, and arising from his work on botanical arithmetic, he supposed that diversity allowed more places to be occupied in a given region. So isolation was not regarded as essential. Large regions with intense competition, and with ample variation spread by blending, would facilitate speciation. The notion of place was different from niche, and it is questioned whether Darwin's views on ecology were as modern as is commonly supposed. Two notions of struggle are found in Darwin's theory; and three notions of variation. Criticisms of his theory led him to emphasize the importance of variation over a range of forms. Hence the theory was populational rather than typological. The theory required a Lamarckian notion of inheritable changes initiated by the environment as a source of variation. Also, Darwin deployed a use/habit theory; and the notion of sexual selection. Selection normally acted at the level of the individual, though kin selection was possible. Group selection was hinted at for man. Darwin's thinking (and also the exposition of his theory) was generally guided by the domestic-organism analogy, which satisfied his methodological requirement of a vera causa principle.     

Thoughts on the origin and nature of life and intelligence on earth

Believing, for good reasons, that our Universe engenders the occurrence of Life, it is probable that Life appeared more than once on young planet Earth. The universality of our genetic code indicates though, that only one line produced a population that was cellular, autopoietic, responsive intelligently (i.e., to its advantage) to its environment, and capable of reproduction. Its evolution took time during which other intermediate or incipient forms of life disappeared. Trying to retrace ab initio the preceding chemical evolution on our young planet, we may not repeat the chemistry which led to our line. One can argue that it may be profitable to attempt to construct artificial life forms using the kind of building blocks that we learned to know through studying the chemistry of our life. Independently, computers are being built, or are planned, which possess memory that can be used appropriately (intelligently), and which to some extent can repair and reproduce themselves. Such Life does not depend on our biochemistry. However, these machines do perform as yet only partly along the lines of our human intelligence which is guided by self-awareness and a sense of individual integrity, and are thereby not equipped to search for Understanding and Self-expression.     

Actin genes expressed during early development ofPatella vulgata

Summary The actin gene family of the marine molluscPatella vulgata was chosen as a model system to study the regulation of genes expressed during early development in molluscs. Using a hamster actin cDNA clone as a probe, we isolated nine actin cDNA clones from trochophore larvae. The total nucleic acid sequence of three of these clones has been determined. Each clone contains the whole protein encoding region. The deduced amino acid sequences resemble actin proteins from other species to a high extent. The nucleotide sequence from the 3UTR (UnTranslated Region) and 5UTR from all nine clones has been resolved. In this way we could identify four different subtypes. Southern blots with genomic DNA were probed with different 3UTR's corresponding to each subtype to determine the genomic organization. One 3UTR detected one band probably corresponding with one gene. Another 3UTR detected one or two genes and the third 3UTR between two and four genes. Northern blots were used to detect the presence of actin mRNA during different stages of development. In the mature oocyte, actin mRNA is present in low amounts. The level of actin mRNA starts to rise steadily from 8 h after fertilization (88-cell stage) onwards. The level of the different subtype mRNAs, as specified by their 3UTR rises at different developmental stages and to various extents. This indicates that the expression of each type is regulated independently and in relation to the developmental stage of the embryo. Correspondence to: A.E. van Loon     

Sialidase of swine influenza A viruses: variation of the recognition specificities for sialyl linkages and for the molecular species of sialic acid with the year of isolation

The sialidase of swine influenza A viruses of N1 and N2 subtypes, isolated from 1930 to 1992, was studied for substrate specificity with ganglio-series, lacto-series type II and GM3 gangliosides containing Neu5Ac2-3Gal, Neu5Gc2-3Gal and Neu5Ac2-6Gal linkages. All viral sialidases tested showed that the activity for hydrolysing substrates with Neu5Ac2-3Gal was higher than the activities with Neu5Gc2-3Gal and Neu5Ac2-6Gal linkages. When GM1b, GM3 and sialylparagloboside were used as substrates, the earliest strain (A/Wisconsin/15/30 H1N1, isolated in 1930) showed the activity ratio of Neu5Ac2-6Gal to Neu5Ac2-3Gal to be 0.13:0.2, and the ratio Neu5Gc2-3Gal/Neu5Ac2-3Gal to be 0.19:0.37, while those strains isolated from 1978 to 1992 exhibited ratios of 0.29:0.58 for Neu5Ac2-6Gal/Neu5Ac2-3Gal and 0.51:0.76 for Neu5Gc2-3Gal/Neu5Ac2-3Gal. The above results indicate that the substrate specificities of sialidases from swine influenza A viruses towards sialyl linkages and the molecular species of sialic acid are related to the year of isolation, i.e. strains isolated after 1978 exhibited higher activity towards Neu5Ac2-6Gal and Neu5Gc2-3Gal linkages when compared with strains isolated in an earlier year, 1930.Abbreviation Neu5Ac 5-N-acetylneuraminic acid - Neu5Gc 5-N-glycolyneuraminic acid - Gal d-galactose - Glc d-glucose - Cer Ceramide - II³(Neu5Ac)Lac Neu5Ac2-3Gal1-4Glc - GM3(Neu5Ac2-3Gal) Neu5Ac2-3Gal1-4Glc1-Cer - GM3(Neu5Gc2-3Gal) Neu5Gc2-3Gal1-4Glc1-Cer - GM1b(Neu5Ac2-3Gal) Neu5Ac2-3Gal1-3GalNac1-4Gal1-4Glc1-Cer - GMlb(Neu5Gc2-3Gal) Neu5Gc2-3Gal1-3GalNAc1-4Gal1-4Glc1-Cer - IV³(Neu5Ac)nLc4Cer Neu5Ac2-3Gal1-3GlcNAc1-4Gal1-4Glc1-Cer - IV³(Neu5Gc)nLc4Cer Neu5Gc2-3Gal1-3GlcNAc1-4Gal1-4Glc1-Cer - IV⁶(Neu5Ac)nLc4Cer Neu5Ac2-6Gal1-3GlcNAc1-4Gal1-4Glc1-Cer - TDC taurodeoxycholate.     

Synthesis of hydroxamic acids using SynPhase? crowns: Development of the hydroxylamine trityl linker

The synthesis of peptide and small molecule hydroxamic acids utilising SynPhase crowns is demonstrated. A hydroxylamine trityl linker is generated from chlorotrityl derivatised Synphase crowns by reaction with N-hydroxyphthalimide followed by subsequent deprotection. The loading of hydroxylamine crowns is quantified spectrophotometrically by measuring phthalhydrazide absorbance at 346 nm.     

Comparative study of the antitumor effect of two types of murine recombinant interferons, (β) and (γ), against B16-F10 melanoma

Summary A comparative study of the antitumor effect of murine recombinant interferon() Mu-rIFN() and murine recombinant interferon() Mu-rIFN() on B16-F10 melanoma was conducted. Administration of Mu-rIFN() i.p. into C57BL/6 mice on days 1 to 7 produced a higher suppressive effect than Mu-rIFN() both on the growth of s.c. implanted tumor and on the formation of artificial pulmonary metastasis. Pharmacokinetic study of Mu-rIFN() demonstrated that high plasma levels were retained for a long time. In clonogenic assay, Mu-rIFN() at 1000 units/ml showed about 80% inhibition of colonies of B16-F10 melanoma. However, Mu-rIFN() hardly inhibited the colonies, even at 1000 units/ml. Augmentation of natural killer (NK) cytotoxicity was much greater with Mu-rIFN() than Mu-rIFN(), whereas Mu-rIFN() enhanced the cytotoxicity of peritoneal macrophages more strongly than Mu-rIFN(). Injection of Mu-rIFN() i.p. 1 day before tumor challenge also inhibited the formation of pulmonary metastasis of B16-F10 melanoma. However, pretreatment of mice with carrageenan significantly suppressed the inhibitory effect of Mu-rIFN(). From these results, it is suggested that the inhibitory effect of Mu-rIFN() on the tumor growth and metastases of B16-F10 melanoma is mediated partly by direct antitumor effect and partly by the activation of macrophages, and that the augmentation of NK activity contributes mainly to the antitumor effect of Mu-rIFN().