Crystal structure of a group I ribozyme domain: principles of RNA packing

Group I self-splicing introns catalyze their own excision from precursor RNAs by way of a two-step transesterification reaction. The catalytic core of these ribozymes is formed by two structural domains. The 2.8-angstrom crystal structure of one of these, the P4-P6 domain of the Tetrahymena thermophila intron, is described. In the 160-nucleotide domain, a sharp bend allows stacked helices of the conserved core to pack alongside helices of an adjacent region. Two specific long-range interactions clamp the two halves of the domain together: a two-Mg2+-coordinated adenosine-rich corkscrew plugs into the minor groove of a helix, and a GAAA hairpin loop binds to a conserved 11-nucleotide internal loop. Metal- and ribose-mediated backbone contacts further stabilize the close side-by-side helical packing. The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.

A phosphatidylinositol (PI) kinase gene family in Dictyostelium discoideum: biological roles of putative mammalian p110 and yeast Vps34p PI 3-kinase homologs during growth and development

Three groups of phosphatidylinositol (PI) kinases convert PI into PI(3)phosphate, PI(4)phosphate, PI(4,5) bisphosphate, and PI(3,4,5)trisphosphate. These phosphoinositides have been shown to function in vesicle-mediated protein sorting, and they serve as second-messenger signaling molecules for regulating cell growth. To further elucidate the mechanism of regulation and function of phosphoinositides, we cloned genes encoding five putative PI kinases from Dictyostelium discoideum. Database analysis indicates that D. discoideum PIK1 (DdPIK1), -2, and -3 are most closely related to the mammalian p110 PI 3-kinase, DdPIK5 is closest to the yeast Vps34p PI 3-kinase, and DdPIK4 is most homologous to PI 4-kinases. Together with other known PI kinases, a superfamily of PI kinase genes has been defined, with all of the encoded proteins sharing a common highly conserved catalytic core domain. DdPIK1, -2, and -3 may have redundant functions because disruption of any single gene had no effect on D. discoideum growth or development. However, strains in which both of the two most highly related genes, DdPIK1 and DdPIK2, were disrupted showed both growth and developmental defects, while double knockouts of DdPIK1 and DdPIK3 and DdPIK2 and DdPIK3 appear to be lethal. The delta Ddpik1 delta Ddpik2 null cells were smaller than wild-type cells and grew slowly both in association with bacteria and in axenic medium when attached to petri plates but were unable to grow in suspension in axenic medium. When delta Ddpik1 delta Ddpik2 null cells were plated for multicellular development, they formed aggregates having multiple tips and produced abnormal fruiting bodies. Antisense expression of DdPIK5 (a putative homolog of the Saccharomyces cerevisiae VPS34) led to a defect in the growth of D. discoideum cells on bacterial lawns and abnormal development. DdPIK5 complemented the temperature-sensitive growth defect of a Schizosaccharomyces pombe delta Svps34 mutant strain, suggesting DdPIK5 encodes a functional homolog of yeast Vps34p. These observations indicate that in D. discoideum, different PI kinases regulate distinct cellular processes, including cell growth, development, and protein trafficking.

[Study on cells associated with human liver fibrosis]

The cells which related to deposition of extracellular matrix (ECM) in human liver fibrogenesis were investigated with immunohistochemistry (IHC) and nucleic acid hybridization. Results showed that ECMs were high in chronic liver disease (CLD) tissues, particularly collagen III and its mRNA in active-CLD. In this group, cells positive for pre-collagen III pro-peptide (PIIIP) and collagen III mRNA were markedly increased and mostly located in the area connecting interstitium and parenchyma. These collagen producing cells were mainly the interstitial cells identified by IHC and electron microscopy as fat storing cells and associated myofibroblasts and fibroblasts. Their degree of hyperplasia was closely related to the infiltration of inflammatory cells.

[CT examination for renal vein thrombosis in nephrotic syndrome and the effect of thrombolytic therapy]

Renal vein thrombosis (RVT) was diagnosed in 12 of 60 patients with nephrotic syndrome with CT scan and confirmed by selective renal angiography. Of the 60 patients, 50 had primary glomerulonephritis with various pathological findings and 10 lupus nephritis. CT is valuable in screening renal vein thrombosis. Renal vein and cubital vein blood in the 12 patients were drawn for assay of FDP, AT III, VIIIR: AG, fibrinogen; the results indicated the presence of a state of hypercoagulation. Of these, 7 were given 200,000 units of urokinase (UK) in divided doses into renal vein within one hour and 5,200,000 units UK into renal artery in the same way. Patients also received 2.5mg/d warfarin and 75mg/d persantine. Except for the 3 with focal sclerosis, patients received 40mg/d prednisone. After 1 month CT and blood fibrinogen, FDP, AT III, VIIIR: AG studies were repeated. RVT in patients with intraarterial UK had complete dissolution of their thrombi. Complete dissolution occurred in 2 of the 7 receiving UK by renal vein and there was partial dissolution in the other 5. It seems that intraarterial injection yielded better results. Hypercoagulation state was alleviated in all patients with UK therapy.

[Investigation of blood supply of bronchogenic carcinoma deriving from pulmonary artery]

Microfil perfusion technique was used to investigate the blood supply of bronchogenic carcinoma deriving from pulmonary artery on 20 fresh specimens of lung cancer, including 11 squamous carcinoma, 6 adenocarcinoma, 1 alveolar cell carcinoma and 2 undifferentiated carcinoma cases. The results showed that the appearance and quantity of pulmonary blood supply of bronchogenic carcinoma depended on and changed with the site, activity, growth mode as well as the local condition of tumor nodules; pulmonary artery supplied blood to the periphery of the tumor and its innermost part as well; vessels from pulmonary artery in tumor nodules were generally less in number than those in the surrouding normal lung tissues around. The results suggested that the tumor blood supply from pulmonary artery should be evaluated comprehensively and dynamically; during interventional chemotherapy via pulmonary artery, patients should be selected carefully and the catheter for infusion placed in suitable position so as to gain the best therapeutic effect.

Cloning and targeted mutations of G alpha 7 and G alpha 8, two developmentally regulated G protein alpha-subunit genes in Dictyostelium

GTP-binding protein (G protein)-mediated signal transduction pathways play essential roles during the aggregation and differentiation process of Dictyostelium. In addition to the five known G protein alpha-subunit genes, we recently identified three novel alpha-subunit genes, G alpha 6, G alpha 7, and G alpha 8, using the polymerase chain reaction technique. We present here a more complete analysis of G alpha 7 and G alpha 8. The cDNAs of these two genes were cloned, and their complete nucleotide sequences were determined. Sequence analyses indicate that G alpha 8 possesses some unusual features. It lacks the "TCATDT" motif, a sequence of amino acids highly conserved among G alpha subunits, and has an additional 50 amino acids at its C-terminus consisting of long stretches of asparagine. Moreover, G alpha 8 is unusually resistant to protease digestion, which may indicate a slow GTP hydrolysis rate. The possible functions of these alpha-subunits were assessed by generating mutants lacking G alpha 7 or G alpha 8 by gene targeting through homologous recombination and by overexpressing G alpha 7 or G alpha 8 protein. Overexpression of G alpha 7 resulted in abnormal morphogenesis starting at the slug stage, whereas analysis of the other strains failed to reveal any obvious growth or developmental defects under either normal or stressful conditions. The implications of these results are discussed.

Structure of trichosanthin at 1.88 A resolution

Trichosanthin (TCS) is one of the single chain ribosome-inactivating proteins (RIPs). The crystals of the orthorhombic form of trichosanthin have been obtained from a citrate buffer (pH 5.4) with KCl as the precipitant. The crystal belongs to the space group P2(1)2(1)2(1) with a = 38.31, b = 76.22, c = 79.21 A. The structure was solved by molecular replacement method and refined using the programs XPLOR and PROLSQ to an R-factor of 0.191 for the reflections within the 6-1.88 A resolution range. The bond length and bond angle in the protein molecule have root-mean-square deviations from ideal value of 0.013 A and 3.3 degrees, respectively. The refined model includes 247 residues and 197 water molecules. The TCS molecule consists of two structural domains. The large domain contains six alpha-helices, a six-stranded sheet, and an antiparallel beta-sheet. The small domain has a largest alpha-helix, which shows a distinct bend. The possible active site of the molecule located on the cleft between two domains was proposed. In the active site Arg-163 and Glu-160, Glu-189 and Arg-122 form two ion pairs, Glu-189 and Gln-156 are hydrogen bonded to each other. Three water molecules are bonded to the residues in the active site region. The structures of TCS molecule and ricin A-chain (RTA) superimpose quite well, showing that the structures of the two protein molecules are homologous. Comparison of the structures of the TCS molecule in this orthorhombic crystal with that in the monoclinic crystal indicates that there are no essential differences of the structures between the two protein crystals.

DRB, DQA, DQB and DPB nucleotide sequences of Saguinus oedipus B95-8

We present eight new nucleotide sequences derived from the second exons of class II genes within the major histocompatibility complex of Sanguinus oedipus (cotton-top tamarin). These comprise two DRB alleles (Saoe-DRB3*0504, -DRB*w1203), two DQA1 alleles (Saoe-DQA1*2501, -DQA1*2502), two DQB1 alleles (Saoe-DQB1*2201, -DQB1*2301), one DQB2 allele (Saoe-DQB2*0101) and one DPB1 allele (Saoe-DPB1*0101).

Indirect latex contact causes urticaria/anaphylaxis

Recurrent urticaria/anaphylaxis is a most perplexing and critical problem, often of unknown cause. Though difficult and time consuming, identification of causes(s) can be life saving and cost saving for the patient(s). We report a complex case of urticaria/anaphylaxis induced by latex allergen in a former intensive care unit nurse, in which the allergen contact occurred remotely and indirectly by intimate contact with the spouse. Diagnosis of the latex allergy was confirmed by epicutaneous skin test in vivo as well as RAST.

Biocompatibilities of organic solvents with Lactobacillus delbrueckii

In the search for biocompatible extractants for extractive fermentation of lactic acid, the effect of twelve organic solvents on the activity of L. delbrueckii were studied at different concentration levels. On this basis, the compatibilities of twelve solvents with L. delbrueckii were summarized into four classes: completely compatible, compatible at molecular level, partially compatible and non-compatible. The characteristics were described qualitatively for each class in terms of relative values between the solubility of organic solvent in water (Cs) and the toxicity of organic solvent, which is indicated by a newly defined concentration parameter (Cm). The classification was helpful for the selection of extractant in extractive fermentation.

Nucleotide sequencing of HLA-DQ gene second exons in Chinese homozygous cells

Six HLA class I and class II-homozygous Chinese cell lines with unique HLA-Dw types were studied. Since the majority of HLA class II nucleotide sequence polymorphism is localized within the second exons of the genes, we used the polymerase chain reaction (PCR) to amplify these regions in HLA-DQA and DQB genes and subsequently determined the nucleotide sequences. No unique DQA1 or DQB1 alleles were found. However, a new haplotype of DQA1*0601-DQB1*0301-DRB1*1202 was found in two cells; and DQA1*03011 was found in association with DR9 in another two cells. This indicates that new DR-DQ associations may explain the observed new HLA-Dw types. The DQB2 sequences were identical in all six cells and were identical to a sequence previously reported in a DR6 haplotype. The DQA2 sequences from two clones obtained from two cells differed from each other and from previously reported sequences. The results show that the DQA1 and DQB1 alleles in the Chinese individuals studied are as previously reported in Caucasian populations and as such may be typed by restriction fragment-length polymorphism (RFLP) or PCR-sequence-specific oligonucleotide typing (PCR-SSO) or PCR-RFLP using conventional probe or restriction enzyme sets.

X-ray studies reveal lanthanide binding sites at the A/B5 interface of E. coli heat labile enterotoxin

The crystal structure determination of heat labile enterotoxin (LT) bound to two different lanthanide ions, erbium and samarium, revealed two distinct ion binding sites in the interface of the A subunit and the B pentamer of the toxin. One of the interface sites is conserved in the very similar cholera toxin sequence. These sites may be potential calcium binding sites. Erbium and samarium binding causes a change in the structure of LT: a rotation of the A1 subunit of up to two degrees relative to the B pentamer.

[Keshan disease and the selenium content of grains in Yunnan province]

The selenium content of 518 specimens of rice, wheat, maize, soybean and highland barley growing both in Keshan disease area and other places in Yunnan Province, was determined and it was found that the average selenium content of the grains in the Keshan disease area was lower than that in the other places. The selenium content of rice especially was much lower than that of wheat and soybean. The relationship of Keshan disease to the low selenium content of grains, especially rice, the most eaten grain by people in the disease area, seemed clearly established in Yunnan province as well.

Image restoration using multigrid methods

In this paper, we discuss several iterative methods for solving the system of linear equations that arises in the process of solving a Fredholm integral equation of the first kind. When applied to the very large systems that arise in connection with two- or three-dimension signal reconstructions, direct methods based on the singular-value decomposition require too much computation and conventional single grid iterative schemes may converge too slowly. We have developed a multigrid scheme in which the solution is sought on a fine grid, but discretizations on a set of coarser grids are used for intermediate calculations to reduce the overall computation effort. Although the quality of the reconstruction obtained using such methods is typically not as good as that achieved using a singular-value decomposition based method, computational considerations should make multigrid methods appealing for large systems of equations.

Structure of yeast regulatory gene LEU3 and evidence that LEU3 itself is under general amino acid control

Determination of the nucleotide sequence of a DNA region from Saccharomyces cerevisiae previously shown to contain the LEU3 gene revealed one long open reading frame (ORF) whose 887 codons predict the existence of a protein with a molecular mass of 100,162 daltons. The codon bias index of 0.02 suggests that LEU3 encodes a low-abundance protein. The predicted amino acid sequence contains a stretch of 31 residues near the N-terminus that is rich in cysteines and basic amino acids and shows strong homology to similar regions in five other regulatory proteins of lower eukaryotes. Additional regions with a predominance of basic amino acids are present adjacent to the cysteine-rich region. A stretch of 20 residues, 19 of which are glu or asp, is found in the carboxy terminal quarter of the protein. The 5' flanking region of LEU3 contains a TATA box 111 bp upstream from the beginning of the long ORF and two transcription initiation elements (5'TCAA3') 58 and 48 bp upstream from the ORF. The 3' flanking region shows a tripartite potential termination-polyadenylation signal. The predicted 5' and 3' ends of the transcript are in very good agreement with the previously determined size of the LEU3 message. Analysis of a LEU3'-'lacZ translational fusion suggests that the LEU3 gene, whose product is involved in the specific regulation of the leucine and possibly the isoleucine-valine pathways, is itself under general amino acid control. Consistent with this observation is the finding that the 5' flanking region of LEU3 contains two perfect copies of the general control target sequence 5'TGACTC3'.