Deriving structural information from non-coding ribonucleic acids by mass spectrometry

The purpose of this study is to describe the development of application of mass spectrometry for the structural analyses of non-coding ribonucleic acids during past decade. Mass spectrometric methods are compared of traditional gel electrophoretic methods, the characteristics of performance of mass spectrometric, analyses are studied and the future trends of mass spectrometry of ribonucleic acids are discussed. Non-coding ribonucleic acids are short polymeric biomolecules which are not translated to proteins, but which may affect the gene expression in all organisms. Regulatory ribonucleic acids act through transient interactions with key molecules in signal transduction pathways. Interactions are mediated through specific secondary and tertiary structures. Posttranscriptional modifications in the structures of molecules may introduce new properties to the organism, such as adaptation to environmental changes or development of resistance to antibiotics. In the scope of this study, the structural studies include i) determination of the sequence of nucleobases in the polymer chain, ii) characterisation and localisation of posttranscriptional modifications in nucleobases and in the backbone structure, iii) identification of ribonucleic acid-binding molecules and iv) probing of higher order structures in the ribonucleic acid molecule. Bacteria, archaea, viruses and HeLa cancer cells have been used as target organisms. Synthesised ribonucleic acids consisting of structural regions of interest have been frequently used. Electrospray ionisation (ESI) and matrix-assisted laser desorption ionisation (MALDI) have been used for ionisation of ribonucleic analytes. Ammonium acetate and 2-propanol are common solvents for ESI. Trihydroxyacetophenone is the optimal MALDI matrix for ionisation of ribonucleic acids and peptides. Ammonium salts are used in ESI buffers and MALDI matrices as additives to remove cation adducts. Reverse phase high performance liquid chromatography has been used for desalting and fractionation of analytes either off-line of on-line, coupled with ESI source. Triethylamine and triethylammonium bicarbonate are used as ion pair reagents almost exclusively. Fourier transform ion cyclotron resonance analyser using ESI coupled with liquid chromatography is the platform of choice for all forms of structural analyses. Time-of-flight (TOF) analyser using MALDI may offer sensitive, easy-to-use and economical solution for simple sequencing of longer oligonucleotides and analyses of analyte mixtures without prior fractionation. Special analysis software is used for computer-aided interpretation of mass spectra. With mass spectrometry, sequences of 20-30 nucleotides of length may be determined unambiguously. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Sequencing in conjunction with other structural studies enables accurate localisation and characterisation of posttranscriptional modifications and identification of nucleobases and amino acids at the sites of interaction. High throughput screening methods for RNA-binding ligands have been developed. Probing of the higher order structures has provided supportive data for computer-generated three dimensional models of viral pseudoknots. In conclusion. mass spectrometric methods are well suited for structural analyses of small species of ribonucleic acids, such as short non-coding ribonucleic acids in the molecular size region of 20-30 nucleotides. Structural information not attainable with other methods of analyses, such as nuclear magnetic resonance and X-ray crystallography, may be obtained with the use of mass spectrometry. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Ligand screening may be used in the search of possible new therapeutic agents. Demanding assay design and challenging interpretation of data requires multidisclipinary knowledge. The implement of mass spectrometry to structural studies of ribonucleic acids is probably most efficiently conducted in specialist groups consisting of researchers from various fields of science.

Temple Emanuel (Andover, Mass.) records, 1939-2001; and Part II (addendum), undated 1952-2004

Temple Emanuel was founded in 1920 in Lawrence, Massachusetts. It began by serving a small immigrant Jewish community that has since grown to an affluent and lively congregation of about 600 families. This growth occurred largely under the tenure of Rabbi Harry A. Roth, who lead the congregation from 1962 until 1990 and oversaw the temple’s move to Andover, Massachusetts. This collection includes correspondence, photographs, and sermons.

The structures of ethyl 1,2,2-tricyano-3,3-dimethylcyclopropane-1-carboxylate and ethyl 2',3,3'-tricyanocyclohexanespirocyclopropane-2'-carboxylate

The crystal and molecular structures of C ,,H,IN302 (I) and C14HIsN302 (II) have been determined by direct methods using three-dimensional X-ray diffractometer data. Crystals of (I) are orthorhombic, space group Pna21, with a = 14.662(6), b = 10.492(5), c = 7.375 (3)A, Z = 4, V = 1134.5 A 3, D O = 1.25 (by flotation), D e = 1.269 Mgm -a, g(MoKa) = 0.085 mm -1. Crystals of (II) are monoclinic, space group P21/a, with a = 7.886 (5), b = 22.011 (8), c = 8.100 (3) A, fl = 103.12 (5) °, Z = 4, V = 1369.2 A 3, D O = 1.23 (by flotation), D e = 1.255 Mg m -3, g(Mo Kct) = 0.080 mm -1. Least-squares full-matrix refinement based on 782 (I) and 1400 independent reflections (II) converged at R = 0.040 (I) and 0.042 (II). The effect of electron-withdrawing substituents on the geometry of the cyclopropane ring is discussed.

Immunologic studies on nucleic acids and their components II. Reversible inhibition of anti-nucleoside antibodies in aqueous pyridine and its application in antibody purification

The effect of aqueous pyridine on a hapten—antihapten system was investigated by the quantitative precipitin reaction and by the membrane filtration method. It was found that dilute solutions of pyridine inhibited the reaction between isopentenyladenosine and its antiserum. Other solvents examined were less effective. The effect of pyridine was reversible at concentrations where complete inhibition occurred, thus indicating its use for the dissociation of antigen—antibody complexes. The inhibitory effect of pyridine was exploited in a single-step purification method for anti—isopentenyladenosine and antideoxy-adenylate antibodies. In addition, generally applicable methods for linking nucleosides and nucleotides to aminoethyl-Sepharose are described.

Formal description, compression and transformation of digital pictures II. Picture algebra and geometry

In an earlier paper (Part I) we described the construction of Hermite code for multiple grey-level pictures using the concepts of vector spaces over Galois Fields. In this paper a new algebra is worked out for Hermite codes to devise algorithms for various transformations such as translation, reflection, rotation, expansion and replication of the original picture. Also other operations such as concatenation, complementation, superposition, Jordan-sum and selective segmentation are considered. It is shown that the Hermite code of a picture is very powerful and serves as a mathematical signature of the picture. The Hermite code will have extensive applications in picture processing, pattern recognition and artificial intelligence.

Mononitrosalted and phenylamido substituted chelate linkage isomers of quadridentate Schiff base copper(II) complexes

The nitrosation of monophenylamido substututed quadridentate Schiff base complexes of copper(II) are observed to adopt N-bonded isonitroso coordination whereas the phenylisocyanation of the corresponding mononitrosated quadridentate complexes are found to prefer O-bonded isonitroso coordination.

Floristic composition and pasture condition of Aristida/Bothriochloa pastures in central Queensland. II. Soil and pasture condition interactions

Sustainable management of native pastures requires an understanding of what the bounds of pasture composition, cover and soil surface condition are for healthy pastoral landscapes to persist. A survey of 107 Aristida/Bothriochloa pasture sites in inland central Queensland was conducted. The sites were chosen for their current diversity of tree cover, apparent pasture condition and soil type to assist in setting more objective bounds on condition ‘states’ in such pastures. Assessors’ estimates of pasture condition were strongly correlated with herbage mass (r = 0.57) and projected ground cover (r = 0. 58), and moderately correlated with pasture crown cover (r = 0.35) and tree basal area (r = 0.32). Pasture condition was not correlated with pasture plant density or the frequency of simple guilds of pasture species. The soil type of Aristida/Bothriochloa pasture communities was generally hard-setting, low in cryptogam cover but moderately covered with litter and projected ground cover (30–50%). There was no correlation between projected ground cover of pasture and estimated ground-level cover of plant crowns. Tree basal area was correlated with broad categories of soil type, probably because greater tree clearing has occurred on the more fertile, heavy-textured clay soils. Of the main perennial grasses, some showed strong soil preferences, for example Tripogon loliiformis for hard-setting soils and Dichanthium sericeum for clays. Common species, such as Chrysopogon fallax and Heteropogon contortus, had no strong soil preference. Wiregrasses (Aristida spp.) tended to be uncommon at both ends of the estimated pasture condition scale whereas H. contortus was far more common in pastures in good condition. Sedges (Cyperaceae) were common on all soil types and for all pasture condition ratings. Plants identified as increaser species were Tragus australianus, daisies (Asteraceae) and potentially toxic herbaceous legumes such as Indigofera spp. and Crotalaria spp. Pasture condition could not be reliably predicted based on the abundance of a single species or taxon but there may be scope for using integrated data for four to five ecologically contrasting plants such as Themeda triandra with daisies, T. loliiformis and flannel weeds (Malvaceae).

Strategic tillage in no-till farming systems in Australia’s northern grains-growing regions: II. Implications for agronomy, soil and environment

In semi-arid sub-tropical areas, a number of studies concerning no-till (NT) farming systems have demonstrated advantages in economic, environmental and soil quality aspects over conventional tillage (CT). However, adoption of continuous NT has contributed to the build-up of herbicide resistant weed populations, increased incidence of soil- and stubble-borne diseases, and stratification of nutrients and organic carbon near the soil surface. Some farmers often resort to an occasional strategic tillage (ST) to manage these problems of NT systems. However, farmers who practice strict NT systems are concerned that even one-time tillage may undo positive soil condition benefits of NT farming systems. We reviewed the pros and cons of the use of occasional ST in NT farming systems. Impacts of occasional ST on agronomy, soil and environment are site-specific and depend on many interacting soil, climatic and management conditions. Most studies conducted in North America and Europe suggest that introducing occasional ST in continuous NT farming systems could improve productivity and profitability in the short term; however in the long-term, the impact is negligible or may be negative. The short term impacts immediately following occasional ST on soil and environment include reduced protective cover, soil loss by erosion, increased runoff, loss of C and water, and reduced microbial activity with little or no detrimental impact in the long-term. A potential negative effect immediately following ST would be reduced plant available water which may result in unreliability of crop sowing in variable seasons. The occurrence of rainfall between the ST and sowing or immediately after the sowing is necessary to replenish soil water lost from the seed zone. Timing of ST is likely to be critical and must be balanced with optimising soil water prior to seeding. The impact of occasional ST varies with the tillage implement used; for example, inversion tillage using mouldboard tillage results in greater impacts as compared to chisel or disc. Opportunities for future research on occasional ST with the most commonly used implements such as tine and/or disc in Australia’s northern grains-growing region are presented in the context of agronomy, soil and the environment.

2-Thioacetamido thiazole as an ambidentate ligand. Complexes of Zn(II), Cd(II), Hg(II) and Cu(I)

Metal complexes of thiazoles have been studied in recent years[I-3] because of their biochemical importance[4,5]. However, data on metal complexes of thiazole derivatives containing another coordinating function are limited[2]. We have synthesized and examined the donor characteristics of a new ligand, 2-thioacetamide thiazole (TATZ)(I) towards chlorides and bromides of Zn(II), Cd(II), Hg(II) and Cu(I). The presence of four potential donor atoms and extensive charge delocalization should render TATZ a versatile ligand.

Studies on "Sappe" disease of the silkworm, Bombyx mori : II. Effect of age of larvae on the manifestation of the disease

The effect of age of the larvae on the manifestation of the "Sappe" disease of the silkworm by oral inoculation of different pathogens, viz., Aerobacter cloacae, Pseudomonas boreopolis, Escherichia freundii, Achromobacter delmarvae, A. Superficialis, Pseudomonas ovalis, and Staphylococcus albus was tested. It was found that the reaction of the larva to the pathogen was influenced by its age. Some, e.g., Escherichia freundii, were more lethal when introduced at early stages whereas certain others, e.g., Aerobacter cloacae and Staphylococcus albus, caused maximum damage when invading older larvae. Irrespective of the age of infection, death of the worms mainly occurred during molting and before spinning. The studies also indicated that growth and mortality of the larvae were affected differentially by the pathogens.

Gas-crystal photoreaction: the structures of 4,4'-dimethoxy(thiobenzophenone) (I), C15H14O2S, and 4,4'-bis(dimethylamino)thiobenzophenone (II), C17H20N2S

(I): M r = 258.34, triclinic, Pi, a = 9.810 (3), b=9.635(3), e=15.015(4)A, a=79.11(2), #= 102.38 (3), y = 107.76 (3) o, V= 1308.5 A 3, Z = 4, Din= 1.318 (3) (by flotation in KI solution), D x = 1.311 g cm -3, Cu Ka, 2 = 1.5418/~, g = 20-05 cm -1, F(000) = 544, T---- 293 K, R = 0.074 for 2663 reflections. (II): M r = 284.43, monoclinic, P2~/c, a= 17.029 (5), b=6.706 (5), c= 14.629 (4), t= 113.55 (2) ° , V=1531.4A 3, Z=4, Dm=1.230(5) (by flotation in KI solution), Dx= 1.234gem -3, Mo Ka, 2 = 0.7107 A, g = 1.63 cm-1; F(000) = 608, T= 293 K, R = 0.062 for 855 reflections. The orientation of the C=S chromophores in the crystal lattice and their reactivity in the crystalline state are discussed. The C--S bonds are much shorter than the normal bond length [1.605 (4) (I), 1.665 (8) A (II) cf. 1.71 A].

4-Biphenylyl phenyl thioketone (I), C19H14S, and 1-naphthyl phenyl thioketone (II), C17H12S

(I): Mr=274"39, orthorhombic, Pbca, a = 7.443 (1), b= 32.691 (3), c= 11.828 (2)A, V= 2877.98A 3, Z=8, Din= 1.216 (flotation in KI), D x = 1.266 g cm -3, /~(Cu Ka, 2 = 1.5418 A) = 17.55 cm -1, F(000) = li52.0, T= 293 K, R = 6.8%, 1378 significant reflections. (II): M r = 248.35, orthorhombic, P212~21, a = 5.873 (3), b = 13.677 (3), c = 15-668 (5) A, V = 1260.14 A 3, Z = 4, D,n = 1.297 (flotation in KI), Dx= 1.308 g cm -a, /t(CuKa, 2=1.5418 A) = 19.55 cm -~, F(000) = 520.0, T= 293 K, R = 6.9%, 751 significant reflections. Crystals of (I) and (II) undergo photo-oxidation in the crystallinestate. In (I) the dihedral angle between the phenyl rings of the biphenyl moiety is 46 (1) °. The C=S bond length is 1.611(5) A in (I) and 1.630 (9)/~ in (II). The correlation between molecular packing and reactivity is discussed.

Matrix Decomposition Methods for Data Mining : Computational Complexity and Algorithms

Matrix decompositions, where a given matrix is represented as a product of two other matrices, are regularly used in data mining. Most matrix decompositions have their roots in linear algebra, but the needs of data mining are not always those of linear algebra. In data mining one needs to have results that are interpretable -- and what is considered interpretable in data mining can be very different to what is considered interpretable in linear algebra. --- The purpose of this thesis is to study matrix decompositions that directly address the issue of interpretability. An example is a decomposition of binary matrices where the factor matrices are assumed to be binary and the matrix multiplication is Boolean. The restriction to binary factor matrices increases interpretability -- factor matrices are of the same type as the original matrix -- and allows the use of Boolean matrix multiplication, which is often more intuitive than normal matrix multiplication with binary matrices. Also several other decomposition methods are described, and the computational complexity of computing them is studied together with the hardness of approximating the related optimization problems. Based on these studies, algorithms for constructing the decompositions are proposed. Constructing the decompositions turns out to be computationally hard, and the proposed algorithms are mostly based on various heuristics. Nevertheless, the algorithms are shown to be capable of finding good results in empirical experiments conducted with both synthetic and real-world data.