Pentafluorophenyl phenyl interaction in biphenyl DNA

We prepared and investigated oligonucleotide duplexes of the sequence d(GATGAC(X)(n)GCTAG)d(CTAGC(Y)(n)GTCATC), in which X and Y designate biphenyl- (bph) and pentafluorobiphenyl- ((5F)bph) C-nucleotides, respectively, and n varies from 0-4. These hydrophobic base substitutes are expected to adopt a zipperlike, interstrand stacking motif, in which not only bph/bph or (5F)bph/(5F)bph homo pairs, but also (5F)bph/bph mixed pairs can be formed. By performing UV-melting curve analysis we found that incorporation of a single (5F)bph/(5F)bph pair leads to a duplex that is essentially as stable as the unmodified duplex (n=0), and 2.4 K more stable than the duplex with the nonfluorinated bph/bph pair. The T(m) of the mixed bph/(5F)bph pair was in between the T(m) values of the respective homo pairs. Additional, unnatural aromatic pairs increased the T(m) by +3.0-4.4 K/couple, irrespective of the nature of the aromatic residue. A thermodynamic analysis using isothermal titration calorimetry (ITC) of a series of duplexes with n=3 revealed lower (less negative) duplex formation enthalpies (DeltaH) in the (5F)bph/(5F)bph case than in the bph/bph case, and confirmed the higher thermodynamic stability (DeltaG) of the fluorinated duplex, suggesting it to be of entropic origin. Our data are compatible with a model in which the stacking of (5F)bph versus bph is dominated by dehydration of the aromatic units upon duplex formation. They do not support a model in which van der Waals dispersive forces (induced dipoles) or electrostatic (quadrupole) interactions play a dominant role

Oligodeoxynucleotide Duplexes Containing (5′S)-5′-C-Alkyl-Modified 2′-Deoxynucleosides: Can an Alkyl Zipper across the DNA Minor-Groove Enhance Duplex Stability?

10.1002/hlca.200390311.abs A series of oligonucleotides containing (5′S)-5′-C-butyl- and (5′S)-5′-C-isopentyl-substituted 2′-deoxyribonucleosides were designed, prepared, and characterized with the intention to explore alkyl-zipper formation between opposing alkyl chains across the minor groove of oligonucleotide duplexes as a means to modulate DNA-duplex stability. From four possible arrangements of the alkyl groups that differ in the density of packing of the alkyl chains across the minor groove, three (duplex types I–III, Fig. 2) could experimentally be realized and their duplex-forming properties analyzed by UV-melting curves, CD spectroscopy, and isothermal titration calorimetry (ITC), as well as by molecular modeling. The results show that all arrangements of alkyl residues within the minor groove of DNA are thermally destabilizing by 1.5–3°/modification in Tm. We found that, within the proposed duplexes with more loosely packed alkyl groups (type-III duplexes), accommodation of alkyl residues without extended distorsion of the helical parameters of B-DNA is possible but does not lead to higher thermodynamic stability. The more densely packed and more unevenly distributed arrangement (type-II duplexes) seems to suffer from ecliptic positioning of opposite alkyl groups, which might account for a systematic negative contribution to stability due to steric interactions. The decreased stability in the type-III duplexes described here may be due either to missing hydrophobic interactions of the alkyl groups (not bulky enough to make close contacts), or to an overcompensation of favorable alkyl-zipper formation presumably by loss of structured H2O in the minor groove.

Generation of long, fully modified, and serum-resistant oligonucleotides by rolling circle amplification

Rolling Circle Amplification (RCA) is an isothermal enzymatic method generating single-stranded DNA products consisting of concatemers containing multiple copies of the reverse complement of the circular template precursor. Little is known on the compatibility of modified nucleoside triphosphates (dN*TPs) with RCA, which would enable the synthesis of long, fully modified ssDNA sequences. Here, dNTPs modified at any position of the scaffold were shown to be compatible with rolling circle amplification, yielding long (>1 kb), and fully modified single-stranded DNA products. This methodology was applied for the generation of long, cytosine-rich synthetic mimics of telomeric DNA. The resulting modified oligo-nucleotides displayed an improved resistance to fetal bovine serum.

Multivalency effects in Pseudomonas aeruginosa biofilm inhibition and dispersal by glycopeptide dendrimers targeting lectin LecA

The galactose specific lectin LecA partly mediates the formation of antibiotic resistant biofilms by Pseudomonas aeruginosa, an opportunistic pathogen causing lethal airways infections in immunocompromised and cystic fibrosis patients, suggesting that preventing LecA binding to natural saccharides might provide new opportunities for treatment. Here 8-fold (G3) and 16-fold (G4) galactosylated analogs of GalAG2, a tetravalent G2 glycopeptide dendrimer LecA ligand and P. aeruginosa biofilm inhibitor, were obtained by convergent chloroacetyl thioether (ClAc) ligation between 4-fold or 8-fold chloroacetylated dendrimer cores and digalactosylated dendritic arms. Hemagglutination inhibition, isothermal titration calorimetry and biofilm inhibition assays showed that G3 dendrimers bind LecA slightly better than their parent G2 dendrimers and induce complete biofilm inhibition and dispersal of P. aeruginosa biofilms, while G4 dendrimers show reduced binding and no biofilm inhibition. A binding model accounting for the observed saturation of glycopeptide dendrimer galactosyl groups and LecA binding sites is proposed based on the crystal structure of a G3 dendrimer LecA complex.

Field-Applicable Recombinase Polymerase Amplification Assay for Rapid Detection of Mycoplasma capricolum subsp. capripneumoniae.

Contagious caprine pleuropneumonia (CCPP) is a highly contagious disease caused by Mycoplasma capricolum subsp. capripneumoniae that affects goats in Africa and Asia. Current available methods for the diagnosis of Mycoplasma infection, including cultivation, serological assays, and PCR, are time-consuming and require fully equipped stationary laboratories, which make them incompatible with testing in the resource-poor settings that are most relevant to this disease. We report a rapid, specific, and sensitive assay employing isothermal DNA amplification using recombinase polymerase amplification (RPA) for the detection of M. capricolum subsp. capripneumoniae. We developed the assay using a specific target sequence in M. capricolum subsp. capripneumoniae, as found in the genome sequence of the field strain ILRI181 and the type strain F38 and that was further evidenced in 10 field strains from different geographical regions. Detection limits corresponding to 5 × 10(3) and 5 × 10(4) cells/ml were obtained using genomic DNA and bacterial culture from M. capricolum subsp. capripneumoniae strain ILRI181, while no amplification was obtained from 71 related Mycoplasma isolates or from the Acholeplasma or the Pasteurella isolates, demonstrating a high degree of specificity. The assay produces a fluorescent signal within 15 to 20 min and worked well using pleural fluid obtained directly from CCPP-positive animals without prior DNA extraction. We demonstrate that the diagnosis of CCPP can be achieved, with a short sample preparation time and a simple read-out device that can be powered by a car battery, in <45 min in a simulated field setting.

UHP Metamorphism Documented in Ti-chondrodite- and Ti-clinohumite-bearing Serpentinized Ultramafic Rocks from Chinese Southwestern Tianshan

The southwestern Tianshan (China) metamorphic belt records high-pressure (HP) to ultrahigh-pressure (UHP) conditions corresponding to a cold oceanic subduction-zone setting. Serpentinites enclosing retrogressed eclogite and rodingite occur as lenses within metapelites in the UHP unit, which also hosts coesite-bearing eclogites. Based on the petrology and petrography of these serpentinites, five events are recognized: (1) formation of a wehrlite–harzburgite–dunite association in the mantle; (2) retrograde metamorphism and partial hydration during exhumation of the mantle rocks close to the seafloor; (3) oceanic metamorphism leading to the first serpentinization and rodingitization; (4) UHP metamorphism during subduction; (5) retrograde metamorphism during exhumation together with a second serpentinization. The peak metamorphic mineral assemblage of the serpentinized wehrlite comprises Ti-chondrodite + olivine + antigorite + chlorite + magnetite + brucite. A computed pseudosection for this serpentinized wehrlite shows that the Al content in antigorite is mostly sensititive to temperature but can also be used to constrain pressure. The average XAl = 0·204 ± 0·026 of antigorite (XAl = Al (a.p.f.u.)/8, where Al is in atoms per formula unit for a structural formula M48T34O85(OH)62, and M and T are octahedral and tetrahedral sites, respectively) included in Ti-chondrodite and average XAl = 0·203 ± 0·019 of antigorite in the matrix result in a well-constrained peak metamorphic temperature of 510–530°C. Peak pressures are less precisely constrained at 37 ± 7 kbar. The Tianshan serpentinites thus record UHP metamorphic conditions and represent the deepest subducted serpentinites discovered so far. The retrograde evolution occurs within the stability field of brucite + antigorite + olivine + chlorite and formation of Ti-clinohumite at the expense of Ti-chondrodite has been observed, suggesting isothermal decompression. The resulting P–T path is in excellent agreement with the metamorphic evolution of country rocks, indicating that the UHP unit in Tianshan was subducted and exhumed as a coherent block. To refine the metamorphic path of the ultramafic rocks, we have investigated the stability fields of Ti-chondrodite and Ti-clinohumite using piston-cylinder experiments. A total of 11 experiments were conducted at 25–55 kbar and 600–750°C in a F-free natural system. Combined with previous experiments and information from natural rocks we constructed a petrogenetic grid for the stability of Ti-chondrodite and Ti-clinohumite in F-free peridotite compositions. The formation of Ti-chondrodite in serpentinites requires a minimum pressure of about 26 kbar, whereas in Ti-rich systems it can form at considerably lower pressures. A key finding is that at UHP conditions, F-free Ti-chondrodite or Ti-clinohumite breaks down in the presence of orthopyroxene between 700 and 750°C, at temperatures that are significantly lower than those of the terminal breakdown reactions of these humite minerals. These breakdown reactions are an additional source of fluid during prograde subduction of serpentinites.

Contrasting PT paths within the Barchi-Kol UHP terrain (Kokchetav Complex): Implications for subduction and exhumation of continental crust

The Barchi-Kol terrain is a classic locality of ultrahigh-pressure (UHP) metamorphism within the Kokchetav metamorphic belt. We provide a detailed and systematic characterization of four metasedimentary samples using dominant mineral assemblages, mineral inclusions in zircon and monazite, garnet zonation with respect to major and trace elements, and Zr-in-rutile and Ti-in-zircon temperatures. A typical diamond-bearing gneiss records peak conditions of 49 ± 4 kbar and 950–1000 °C. Near isothermal decompression of this rock resulted in the breakdown of phengite associated with a pervasive recrystallization of the rock. The same terrain also contains mica schists that experienced peak conditions close to those of the diamond-bearing rocks, but they were exhumed along a cooler path where phengite remained stable. In these rocks, major and trace element zoning in garnet has been completely equilibrated. A layered gneiss was metamorphosed at UHP conditions in the coesite field, but did not reach diamond-facies conditions (peak conditions: 30 kbar and 800–900 °C). In this sample, garnet records retrograde zonation in major elements and also retains prograde zoning in trace elements. A garnet-kyanite-micaschist that reached significantly lower pressures (24 ± 2 kbar, 710 ± 20 °C) contains garnet with major and trace element zoning. The diverse garnet zoning in samples that experienced different metamorphic conditions allows to establish that diffusional equilibration of rare earth element in garnet likely occurs at ~900–950 °C. Different metamorphic conditions in the four investigated samples are also documented in zircon trace element zonation and mineral inclusions in zircon and monazite. U-Pb geochronology of metamorphic zircon and monazite domains demonstrates that prograde (528–521 Ma), peak (528–522 Ma), and peak to retrograde metamorphism (503–532 Ma) occurred over a relatively short time interval that is indistinguishable from metamorphism of other UHP rocks within the Kokchetav metamorphic belt. Therefore, the assembly of rocks with contrasting P-T trajectories must have occurred in a single subduction-exhumation cycle, providing a snapshot of the thermal structure of a subducted continental margin prior to collision. The rocks were initially buried along a low geothermal gradient. At 20–25 kbar they underwent near isobaric heating of 200 °C, which was followed by continued burial along a low geothermal gradient. Such a step-wise geotherm is in good agreement with predictions from subduction zone thermal models.

Role of Neurogranin in the regulation of calcium binding to Calmodulin

Role of Neurogranin in the regulation of calcium binding to Calmodulin Anuja Chandrasekar, B.S Advisor: M. Neal Waxham, Ph.D The overall goal of my project was to gain a quantitative understanding of how the interaction between two proteins neurogranin (RC3) and calmodulin (CaM) alters a fundamental property of CaM. CaM, has been extensively studied for more than four decades due to its seminal role in almost all biological functions as a calcium signal transducer. Calcium signals in cardiac and neuronal cells are exquisitely precise and enable activation of some processes while down-regulating others. CaM, with its four calcium binding sites, serves as a central component of calcium signaling in these cells. It is aided in this role as a regulatory hub that differentially activates targets in response to a calcium flux by proteins that alter its calcium binding properties. Neurogranin, also known as RC3, is a member of a family of small neuronal IQ (SNIQ) domain proteins that was originally thought to play a ‘capacitive’ role by sequestering CaM until a calcium influx of sufficient intensity arrived. However, based on earlier work in our lab on neurogranin, we believe that this protein plays a more nuanced role in neurons than simply acting as a CaM buffer. We believe that neurogranin is one of the proteins which, by altering the kinetics of calcium binding allow CaM to decode a variety of signals with fine precision. To quantify the interaction between CaM, neurogranin and calcium, I used biophysical techniques and computational simulations. From my results, I conclude that neurogranin finely regulates the proportion of calcium-saturated CaM and thereby directs CaM’s target specificity.

Proceedings of the Fifteenth Annual biochemical Engineering Symposium

This work represents the proceedings of the fifteenth symposium which convened at Colorado State University on May 24, 1985. The two day meeting was scheduled one month later than usual, i.e., after the spring semester, so that travelers from the Midwest (Iowa State University, Kansas State University and University of Missouri) could enjoy the unique mountain setting provided at Pingree Park. The background of the photograph on the cover depicts the beauty of the area. ContentsGreg Sinton and S.M. Leo, KSU. Models for the Biodegration of 2.4-D and Related Xenobiotic Compounds. V. Bringi, CSU. Intrinsic Kinetics from a Novel Immobilized Cell CSTR. Steve Birdsell, CU. Novel Microbial Separation Techniques. Mark Smith, MU. Kinetic Characterization of Growth of E. coli on Glucose. Michael M. Meagher, ISU. Kinetic Parameters of Di- and Trisaccharaide Hydrolysis by Glucoamylase II. G.T. Jones and A.K. Ghosh Hajra, KSU. Modeling and Simulation of Legume Modules with Reactive Cores and Inert Shells. S.A. Patel and C.H. Lee, KSU. Energetic Analysis and Liquid Circulation in an Airlift Fermenter. Rod R. Fisher, ISU. The Effects of Mixing during Acid Addition of Fractionally Precipitated Protein. Mark M. Paige, CSU. Fed-batch Fermentations of Clostridium acetobutylicum. Michael K. Dowd, ISU. A Nonequilibirium Thermodynamic Description of the Variation of Contractile Velocity and Energy Use in Muscle. David D. Drury, CSU. Analysis of Hollow Fiber Bioreactor Performance for MAmmalian Cells by On-Line MMR. H.Y. Lee, KSU. Process Analysis of Photosynthetic Continuous Culture Systems. C.J. Wang, MU. Kinetic Consideration in Fermentation of Cheese Whey to Ethanol.

Paleomagnetic of the Cobb Mountin event sections

Detailed paleomagnetic investigations are reported for 283 specimens, sampled from three closely spaced Ocean Drilling Program Leg 135 cores from the Lau Basin. These specimens cover three rather similar records of the reversed Cobb Mountain short polarity event, having an age of about 1.12 m.y. On the basis of a very detailed subsampling every 0.6 cm, we found that the transition times for the Cobb Mountain geomagnetic polarity event, as seen in the three Lau Basin sediment records, appear to have been as short as 0.6-1.0 k.y., although the duration of the normal-polarity event itself lasted only about 17 ± 4 k.y. The older (R to N) transition as well as the younger (N to R) transition show virtual geomagnetic paths roughly along the Americas, but shifted some 30° ± 10° to the east. These paths conflict with Cobb Mountain transition paths recorded in sediments from the Labrador Sea and the North Atlantic, but they are in fair accordance with sediment records from the Celebes and Sulu seas when corrected for differences in site longitude, suggesting that the transitional fields are dominated by nonaxial, high-order spherical harmonics.

Ice and snow measurements during Nathaniel B. Palmer cruise NBP0709 (SIMBA experiment)

The Sea Ice Mass Balance in the Antarctic (SIMBA) experiment was conducted from the RVIB N.B. Palmer in September and October 2007 in the Bellingshausen Sea in an area recently experiencing considerable changes in both climate and sea ice cover. Snow and ice properties were observed at 3 short-term stations and a 27-day drift station (Ice Station Belgica, ISB) during the winter-spring transition. Repeat measurements were performed on sea ice and snow cover at 5 ISB sites, each having different physical characteristics, with mean ice (snow) thicknesses varying from 0.6 m (0.1 m) to 2.3 m (0.7 m). Ice cores retrieved every five days from 2 sites and measured for physical, biological, and chemical properties. Three ice mass-balance buoys (IMBs) provided continuous records of snow and ice thickness and temperature. Meteorological conditions changed from warm fronts with high winds and precipitation followed by cold and calm periods through four cycles during ISB. The snow cover regulated temperature flux and controlled the physical regime in which sea ice morphology changed. Level thin ice areas had little snow accumulation and experienced greater thermal fluctuations resulting in brine salinity and volume changes, and winter maximum thermodynamic growth of ~0.6 m in this region. Flooding and snow-ice formation occurred during cold spells in ice and snow of intermediate thickness. In contrast, little snow-ice formed in flooded areas with thicker ice and snow cover, instead nearly isothermal, highly permeable ice persisted. In spring, short-lived cold air episodes did not effectively penetrate the sea ice nor overcome the effect of ocean heat flux, thus favoring net ice thinning from bottom melt over ice thickening from snow-ice growth, in all cases. These warm ice conditions were consistent with regional remote sensing observations of earlier ice breakup and a shorter sea ice season, more recently observed in the Bellingshausen Sea.

Paleomegnetic and geochemistry of sediments from the early Aptian Oceanic Anoxic Event

The early Aptian Oceanic Anoxic Event (OAE1a, 120 Ma) represents a geologically brief time interval in the mid-Cretaceous greenhouse world that is characterized by increased organic carbon accumulation in marine sediments, sudden biotic changes, and abrupt carbon-isotope excursions indicative of significant perturbations to global carbon cycling. The brevity of these drastic environmental changes (< 10**6 year) and the typically 10**6 year temporal resolution of the available chronologies, however, represent a critical gap in our knowledge of OAE1a. We have conducted a high-resolution investigation of three widely distributed sections, including the Cismon APTICORE in Italy, Santa Rosa Canyon in northeastern Mexico, and Deep Sea Drilling Project (DSDP) Site 398 off the Iberian margin in the North Atlantic Ocean, which represent a range of depositional environments where condensed and moderately expanded OAE1a intervals are recorded. The objectives of this study are to establish orbital chronologies for these sections and to construct a common, high-resolution timescale for OAE1a. Spectral analyses of the closely-spaced (corresponding to ~5 to 10 kyr) measurements of calcium carbonate content of the APTICORE, magnetic susceptibility (MS) and anhysteretic remanent magnetization (ARM) of the Santa Rosa samples, and MS, ARM and ARM/IRM, where IRM is isothermal remanent magnetization, of Site 398 samples reveal statistically significant cycles. These cycles exhibit periodicity ratios and modulation patterns similar to those of the mid-Cretaceous orbital cycles, suggesting that orbital variations may have modulated depositional processes. Orbital control allows us to estimate the duration of unique, globally identifiable stages of OAE1a. Although OAE1a had a duration of ~1.0 to 1.3 Myr, the initial perturbation represented by the negative carbon-isotope excursion was rapid, lasting for ~27-44 kyr. This estimate could serve as a basis for constraining triggering mechanisms for OAE1a.

Rock-magnetic proxies from a sediment profile of Aike Lake

The sedimentary archive from Laguna Potrok Aike is the only continuous record reaching back to the last Glacial period in continental southeastern Patagonia. Located in the path of the Southern Hemisphere westerly winds and in the source region of dust deposited in Antarctica during Glacial periods, southern Patagonia is a vantage point to reconstruct past changes in aeolian activity. Here we use high-resolution rock-magnetic and physical grain size data from site 2 of the International Continental scientific Drilling Program (ICDP) Potrok Aike maar lake Sediment Archive Drilling prOject (PASADO) in order to develop magnetic proxies of dust and wind intensity at 52°S since 51,200 cal BP. Rock-magnetic analysis indicate the magnetic mineral assemblage is dominated by detrital magnetite. Based on the estimated flux of magnetite to the lake and comparison with distal dust records from the Southern Ocean and Antarctica, kLF is interpreted as a dust indicator in the dust source of southern Patagonia at the millennial time scale, when ferrimagnetic grain size and coercivity influence is minimal. Comparison to physical grain-size data indicates that the median destructive field of isothermal remanent magnetisation (MDFIRM) mostly reflects medium to coarse magnetite bearing silts typically transported by winds for short-term suspension. Comparison with wind-intensity proxies from the Southern Hemisphere during the last Glacial period and with regional records from Patagonia since the last deglaciation including marine, lacustrine and peat bog sediments as well as speleothems reveals similar variability with MDFIRM up to the centennial time scale. MDFIRM is interpreted as a wind-intensity proxy independent of moisture changes for southeastern Patagonia, with stronger winds capable of transporting coarser magnetite bearing silts to the lake.