SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups

Automated methods have been developed to determine the preferred packing arrangement between interacting protein groups. A suite of FORTRAN programs, SIRIUS, is described for calculating and analysing the geometries of interacting protein groups using crystallographically derived atomic co-ordinates. The programs involved in calculating the geometries search for interacting pairs of protein groups using a distance criterion, and then calculate the spatial disposition and orientation of the pair. The second set of programs is devoted to analysis. This involves calculating the observed and expected distributions of the angles and assessing the statistical significance of the difference between the two. A database of the geometries of the 400 combinations of side-chain to side-chain interaction has been created. The approach used in analysing the geometrical information is illustrated here with specific examples of interactions between side-chains, peptide groups and particular types of atom. At the side-chain level, an analysis of aromatic-amino interactions, and the interactions of peptide carbonyl groups with arginine residues is presented. At the atomic level the analyses include the spatial disposition of oxygen atoms around tyrosine residues, and the frequency and type of contact between carbon, nitrogen and oxygen atoms. This information is currently being applied to the modelling of protein interactions.     

Morphology and distribution of tanycytes in the third ventricle of the adult rat. A study using semithin methacrylate sections

Light microscopy and semithin methacrylate sections were used to study the tanycytic projections and morphology in the floor of the third ventricle of the rat. The tanycytic cell soma was located in the ependyma. The luminal surface showed minute protrusions into the ventricular space and their basal processes projected across the width of the parenchyma of the infundibular region. During their course, tanycytic processes made contact with capillaries in the parenchyma and pial surface, suggesting that they might be involved in uptake and/or delivery mechanisms between the cerebrospinal fluid, hypothalamic cells and blood vessels.     

A specific androgen-binding protein (ABP) in Necturus testis and its zonal distribution

The urodele amphibian Necturus maculosus has a zoned testis, which is advantageous for separating Leydig cells from germinal elements and for studying stage-dependent biochemical changes. Using [3H]testosterone (T) in a standard binding assay and dextran-coated charcoal (DCC) or Sephadex LH-20 to separate free and bound steroids, we identified an androgen-binding protein (ABP) in Necturus testis cytosols. This protein was of high affinity (Kd = 10(-9) M) and was saturable (Bmax = 10(-9) M) and specific for androgen (T; 5 alpha-dihydrotestosterone, DHT) but could be distinguished from the androgen receptor of Necturus testis by its relative abundance (300-550 fmol/mg protein), short half-time of dissociation (3 min at 22 degrees C), inability to adhere to DNA-cellulose, and absence from nuclear extracts. Additionally, when analyzed on sucrose gradients, the ABP of Necturus testis sedimented at 6-7 S in both low or high ionic strength buffers. In that estradiol (E2) is a poor competitor for T-binding, this protein resembles a sex steroid-binding protein previously identified in urodele serum but differs from the ABP and testosterone-estradiol-binding globulin (TEBG) of rodents, humans, goldfish, and sharks. It is differentially distributed within the testis, with the highest levels in immature lobular regions composed of Sertoli cells and germ cells in premeiotic stages and lower levels in regions composed primarily of Leydig cells. The cellular source and function of this protein in Necturus testis remain to be determined.     

The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography.

This study describes the first crystal structures of a complex between a DNA topoisomerase and a drug. We present the structures of a 24 kDa N-terminal fragment of the Escherichia coli DNA gyrase B protein in complexes with two different inhibitors of the ATPase activity of DNA gyrase, namely the coumarin antibiotic, novobiocin, and GR122222X, a member of the cyclothialidine family. These structures are compared with the crystal structure of the complex with an ATP analogue, adenylyl-beta-gamma-imidodiphosphate (ADPNP). The likely mechanism, by which mutant gyrase B proteins become resistant to inhibition by novobiocin are discussed in light of these comparisons. The three ligands are quite dissimilar in chemical structure and bind to the protein in very different ways, but their binding is competitive because of a small degree of overlap of their binding sites. These crystal structures consequently describe a chemically well characterized ligand binding surface and provide useful information to assist in the design of novel ligands.     

Analysis of woody vegetation of Corbett National Park,India

The heterogeneous vegetation mosaic of the South Turkana region of north Kenya is associated with diversity in the region's physical environment. The abundance and distribution of the dominant species are related to gradients in those abiotic factors that influence water availability, including precipitation, soil texture, and topographic relief. Research focused on three Acacia species that are a major component of the Turkana vegetation; A. tortilis, A. senegal, and A. reficiens. These species each exhibit a different response to variations in abiotic factors. Consequently, species abundance varies independently across the landscape, creating a continuum of intergrading populations. Community types can be identified within the mosaic of intergrading populations. Although community borders are not discrete due to continual change in species abundance, types are identifiable and are repeated in areas with similar environmental conditions. The landscape patterns are representative of Whittaker's (1953) climaxas-pattern, with communities created by individual patterns of populations responding to environmental gradients, creating a continuum of community change across the landscape.     

Sublethal malathion induced changes in the ovary of an air-breathing fish,Heteropneustes fossilis: a histological study

This paper describes effects of a sublethal (1.2 mg 1^–1) organophosphate, malathion, on the ovary of an air breathing catfish, Heteropneustes fossilis. The study focuses on microscopic changes that occur on ovigerous lamellae, oocytes at different stages of development and the nucleus of the immature oocyte. Also, change in estrogen levels in blood serum is investigated. Clumping of cytoplasm appears after 24 h of exposure to malathion. Clumping intensified after 48 h. Degeneration in the follicular cells was also observed. After 72 h exposure the number of nucleoli increased, nuclear materials shrunk, oocytes became adhered. With 96 h of exposure, nuclear materials of all the oocytes shrunk to a smaller clump. The oocytes fused together, and follicular epithelium became loose and ruptured. A few atretic oocytes were visible. Radioimmunoassay of the estrogen level in blood serum after 72 h of exposure of malathion showed a reduction in the level. This study showed that the histopathological condition of the gonad is reflected in malfunctioning of the endocrine system and hormonal disbalance.     

Banded krait minor satellite (Bkm) contains sex and species-specific repetitive DNA

A novel class of repetitive DNA was isolated from a Bkm DNA library by exclusion hybridization. This sequence was mapped to the short arm of the W chromosome of banded krait, Bungarus fasciatus. Southern blot hybridization showed that these sequences are sex and species specific. Sequence analysis of a 206 bp long clone, BR87, revealed the presence of a tandem array of two internal repeat units of 18–19 bp alternating with each other with a gap of 1,2 or 3 nucleotides. To our knowledge, this is the first report of an exclusively W chromosome-and species-specific repeat isolated from any reptile. The functional significance of this sequence based on its organisation is discussed.     

Production of disease-free encapsulated buds of Zingiber officinale Rosc.

Shoot buds of ginger were successfully encapsulated in 4% sodium alginate gel. Encapsulated buds were germinated in vitro to form roots and shoots. In vitro germination (emergence of sprouts) of encapsulated buds ranged from 16.7% to 81.8% on different media after 5 weeks of incubation. Normal plantlets with an average shoot length of 2.3 cm and 1.7 cm root length were successfully transplanted into unsterilized soil without any hardening process. These plantlets showed no symptoms of ginger yellows disease and the causal fungal pathogen failed to grow out on culture media (used as a diagnostic test).