Crystallization and preliminary crystallographic studies of the decadeoxyoligonucleotide d(CpGpTpApCpGpTpApCpG)

Crystals of the self-complementary decadeoxyoligonucleotide d(CpGpTpApCpGpTpApCpG) have been grown from a solution containing [Co(NH3)6]Cl3 and spermine. The amber-colored crystals are hexagonal and belong to the space group P6(5) (or P6(1] with unit cell parameters a = 17.93 A, c = 43.41 A. Precession photography and molecular packing considerations indicate that the unit cell consists of a 12 nucleotide duplex. The asymmetric unit, therefore, is a disordered duplex dimer in which each pyrimidine-purine base-pair is occupied 60% of the time by a C . G pair and 40% of the time by a T . A pair. The above considerations and preliminary structure analysis reveal that this alternating pyrimidine-purine oligomer assumes a Z-DNA conformation.     

Murine C4-binding protein: a rapid purification method by affinity chromatography

A simple, 3-step method was described for purification of murine C4 binding protein (C4-bp), a recently recognized serum protein that functions as one of the regulatory proteins of the complement system. The method consists of 1) affinity chromatography using TNBS-BGG-conjugated Sepharose beads, 2) gel filtration on a Sepharose 6B column, and 3) heparin-Sepharose chromatography. By this method, milligram quantities of C4-bp can be easily purified by more than 500-fold from EDTA-serum of various mouse strains, and the whole purification process can be completed within 1 wk. The overall yield of C4-bp is about 15%. The C4-bp thus prepared is homogeneous as judged by SDS-polyacrylamide gel electrophoresis and immunelectrophoresis. The purified mouse C4-bp showed physicochemical properties very similar to those described for human C4-bp. Like human C4-bp, mouse C4-bp is composed of several apparently identical subunits of the m.w. of 80,000. However unlike the human counterpart, the subunits of mouse C4-bp are not linked by disulfide bonds but are connected by non-covalent forces that can be disrupted by SDS. The purified mouse C4-bp retained binding affinity for C4 and showed unaltered antigenicity. Immunization of rabbits with the purified mouse C4-bp resulted in the production of potent and monospecific antisera.     

Cloning and expression of the Erwinia chrysanthemi asparaginase gene in Escherichia coli and Erwinia carotovora

A genomic library of Erwinia chrysanthemi DNA was constructed in bacteriophage lambda 1059 and recombinants expressing Er. chrysanthemi asparaginase detected using purified anti-asparaginase IgG. The gene was subcloned on a 4.7 kb EcoRI DNA restriction fragment into pUC9 to generate the recombinant plasmid pASN30. The position and orientation of the asparaginase structural gene was determined by subcloning. The enzyme was produced at high levels in Escherichia coli (5% of soluble protein) and was shown to be exported to the periplasmic space. Purified asparaginase from E. coli cells carrying pASN30 was indistinguishable from the Erwinia enzyme on the basis of specific activity [660-700 units (mg protein)-1], pI value (8.5), and subunit molecular weight (32 X 10(3]. Expression of the cloned gene was subject to glucose repression in E. coli but was not significantly repressed by glycerol. Recombinant plasmids, containing the asparaginase gene, when introduced into Erwinia carotovora, caused increased synthesis of the enzyme (2-4 fold higher than the current production strain).     

A nuclear specific glycoprotein representative of a unique pattern of glycosylation

Whole rat liver nuclei were reacted with UDP-[14C]galactose in the presence of bovine beta(1----4) galactosyltransferase. The reaction mixture was electrophoresed on a reducing sodium dodecyl sulfate-polyacrylamide gel. Autoradiograms of the gel demonstrated a major labeled broad band migrating with an apparent molecular weight of 65,000-66,000. A number of other less prominently labeled bands were also present. The labeled 65,000-66,000 band when cut from the gel and subjected to alkaline reduction while in the gel matrix exclusively yielded a 14C-labeled disaccharide that co-migrated with a [14C]Gal-GlcNAcol standard in descending paper chromatography. Treatment of this disaccharide with beta-galactosidase (beta-D-galactoside galactohydrolase; EC 3.2.1.23) from Aspergillus niger removed all the [14C]galactose label. Treatment of the labeled 65,000-66,000 polypeptide with Endoglycosidase F, however, did not remove the [14C]galactose label. Western transfer blots of sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels performed with horseradish peroxidase-labeled succinyl wheat germ agglutinin, a lectin specific for GlcNAc, on unlabeled nuclei revealed a dominant band at 63,000-64,000. Subjecting 14C-labeled nuclei to this procedure resulted in a shift of the major horseradish peroxidase-labeled succinyl wheat germ agglutinin band to 65,000-66,000. The shifted band was coincident with the [14C]galactose band as visualized on an autoradiogram. A survey of other rat tissue nuclei revealed the same spectrum of [14C]galactose acceptor proteins with a dominant 65,000-66,000 galactose-labeled band.     

Increased near-ultraviolet induced DNA fragmentation in xeroderma pigmentosum variants.

Immediate fragmentation of parental DNA by near-ultraviolet irradiation at 313 nm was measured in cultured skin fibroblasts from normal individuals, patients with Xeroderma pigmentosum of complementation group A (XPA) and Xeroderma pigmentosum variants (XPV) by the alkaline elution procedure. For a dose of 2.25 KJm^?2 given at O^o fragmentation was comparable in all cell strains. However, fragmentation was strongly increased relative to O^o in XPV but not in normal fibroblasts and the XPA strains when irradiation was carried out at 37^o. From our results it appears that a step in the repair of $\text{parental}$ DNA is abnormal in XPV.     

Antibacterial activity of Turkish propolis and its qualitative and quantitative chemical composition

The antibacterial activity of propolis from different regions of Turkey was studied, accompanied by TLC and GC-MS analyses of its chemical composition and spectrophotometric quantification of the most important active principles. All six samples were active against the bacterial test strains used; however, samples 1 (Yozgat), 2 (Izmir) and 3 (Kayseri) were more active than samples 4 (Adana), 5 (Erzurum) and 6 (Artvin). By TLC comparison all samples were found to contain poplar taxonomic markers but in samples 4 (Adana), 5 (Erzurum) and 6 (Artvin), different substances were observed, which were not present in P. nigra L. bud exudate. The typical poplar samples 1 (Yozgat), 2 (Izmir) and 3 (Kayseri) displayed very similar phenolic and flavonoid content. Samples 4 (Adana), 5 (Erzurum) and 6 (Artvin) were characterized by low phenolic and very low flavonoid concentrations. Qualitative analysis by GC-MS revealed that sample 4 (Adana) contained diterpenic acids and high percent of cinnamyl cinnamate, sample 5 (Erzurum)-significant amounts of hydroxy fatty acids and triterpenic alcohoLs, and sample 6 (Artvin)-phenolic glycerides, characteristic for the bud exudate of Populus euphratica Oliv. The results confirm the importance of phenolics for propolis antibacterial activity, and the significance of P. nigra L. as a propolis source, which provides the hive with the best defense against microorganisms.     

Water inputs across a tropical montane landscape in Veracruz,Mexico: synergistic effects of land cover,rain and fog seasonality,and interannual precipitation variability

Land‐cover change can alter the spatiotemporal distribution of water inputs to mountain ecosystems, an important control on land‐surface and land‐atmosphere hydrologic fluxes. In eastern Mexico, we examined the influence of three widespread land‐cover types, montane cloud forest, coffee agroforestry, and cleared areas, on total and net water inputs to soil. Stand structural characteristics, as well as rain, fog, stemflow, and throughfall (water that falls through the canopy) water fluxes were measured across 11 sites during wet and dry seasons from 2005 to 2008. Land‐cover type had a significant effect on annual and seasonal net throughfall (NTF <0=canopy water retention plus canopy evaporation; NTF >0=fog water deposition). Forest canopies retained and/or lost to evaporation (i.e. NTF<0) five‐ to 11‐fold more water than coffee agroforests. Moreover, stemflow was fourfold higher under coffee shade than forest trees. Precipitation seasonality and phenological patterns determined the magnitude of these land‐cover differences, as well as their implications for the hydrologic cycle. Significant negative relationships were found between NTF and tree leaf area index (R²=0.38, P<0.002), NTF and stand basal area (R²=0.664, P<0.002), and stemflow and epiphyte loading (R²=0.414, P<0.001). These findings indicate that leaf and epiphyte surface area reductions associated with forest conversion decrease canopy water retention/evaporation, thereby increasing throughfall and stemflow inputs to soil. Interannual precipitation variability also altered patterns of water redistribution across this landscape. Storms and hurricanes resulted in little difference in forest‐coffee wet season NTF, while El Niño Southern Oscillation was associated with a twofold increase in dry season rain and fog throughfall water deposition. In montane headwater regions, changes in water delivery to canopies and soils may affect infiltration, runoff, and evapotranspiration, with implications for provisioning (e.g. water supply) and regulating (e.g. flood mitigation) ecosystem services.     

Flux analysis of recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimal ethanol production

Genetically modified Saccharomyces cerevisiae strain (YPB-G) which secretes a bifunctional fusion protein that contains both Bacillus subtilis -amylase and Aspergillus awamori glucoamylase activities was used for the direct conversion of starch into ethanol. Starch was either supplied initially to different nutrient media or added instantaneously to the reactor at various discrete time instants (pulse feeding). Stoichiometric modeling was used to investigate the effects of initial substrate concentration and growth rate of the recombinant yeast culture on ethanol production. Reaction stoichiometries describing both the anabolism and catabolism of the microorganism were used as an input to flux balance analysis (FBA), the preferred metabolic modeling approach since the constructed stoichiometric network was underdetermined. Experiments for batch and fed-batch systems at different substrate concentrations were analyzed theoretically in terms of flux distributions using ethanol production rate as the maximization criteria. Calculated ethanol rates were in agreement with experimental measurements, suggesting that this recombinant microorganism is sufficiently evolved to optimize its ethanol production. The function of the main pathways of yeast metabolism (PPP, EMP, TCA) are discussed together with the node analyses of glucose-6-P and pyruvate branch points. Theoretical node analysis revealed that if the split ratio in G6P branch point is changed by genetic manipulations, the ethanol yield would be affected considerably.