Broadband RFDR with adiabatic inversion pulses

With a view to obtain ¹³C chemical shift correlation spectra of uniformly labelled peptides/proteins at high magnetic fields and high magic angle spinning frequencies (_r/2 20 kHz), the efficacy of RFDR with adiabatic inversion pulses has been assessed via numerical simulations and experimental measurements employing different adiabatic pulse phasing schemes, shapes and durations. It is demonstrated that homonuclear dipolar recoupling with superior performance under resonance offset and H ₁ inhomogeneity effects and without strong dependence on the ¹³C chemical shift differences can be achieved with adiabatic pulses. It is shown that ¹³C chemical shift correlation spectra in the entire range of carbon chemical shifts can be obtained efficiently with short adiabatic inversion pulses. In situations where correlation spectra of only the aliphatic region are required, the possibility for minimising the interference between the recoupling and decoupling RF fields with long adiabatic pulses, at low recoupling power levels and without compromising the broadband RFDR characteristics, is also indicated.     

Three-dimensional structure determination of a uniformly labeled molecule by frequency-selective dipolar recoupling under magic-angle spinning

The complete three-dimensional (3D) structure of a glycylisoleucine (Gly-Ile) molecule was determined by individually measuring six dihedral angles with a frequency-selective homonuclear dipolar recoupling method, R2TR (rotational resonance in the tilted rotating frame), using a powder sample of diluted uniformly 13,15-labeled Gly-Ile. Each dihedral angle was obtained by recoupling a dipolar interaction between three or four bonds distant spins concerned or observing a dipolar correlation 2D powder pattern. The 3D structure of a Gly-Ile molecule was also determined by X-ray crystallography, and a good agreement with the NMR result was obtained. The results demonstrate that the R2TR method in a uniformly labeled powder sample can provide the 3D structure without the need to prepare a lot of selectively labeled samples.     

Efficient solvent suppression with adiabatic inversion for 1H-detected solid-state NMR

This study introduces a conceptually new solvent suppression scheme with adiabatic inversion pulses for ¹H-detected multidimensional solid-state NMR (SSNMR) of biomolecules and other systems, which is termed “Solvent suppression of Liquid signal with Adiabatic Pulse” (SLAP). ¹H-detected 2D ¹³C/¹H SSNMR data of uniformly ¹³C- and ¹⁵N-labeled GB1 sample using ultra-fast magic angle spinning at a spinning rate of 60 kHz demonstrated that the SLAP scheme showed up to 3.5-fold better solvent suppression performance over a traditional solvent-suppression scheme for SSNMR, MISSISSIPPI (Zhou and Rienstra, J Magn Reson 192:167–172, 2008) with 2/3 of the average RF power.

     

TEDOR with adiabatic inversion pulses: Resonance assignments of <Superscript>13</Superscript>C/<Superscript>15</Superscript>N labelled RNAs

We have examined via numerical simulations the performance characteristics of different 15N RF pulse schemes employed in the transferred echo double resonance (TEDOR) experimental protocol for generating 13C-15N dipolar chemical shift correlation spectra of isotopically labelled biological systems at moderate MAS frequencies (omega(r) approximately 10 kHz). With an 15N field strength of approximately 30-35 kHz that is typically available in 5 mm triple resonance MAS NMR probes, it is shown that a robust TEDOR sequence with significant tolerance to experimental imperfections sa as H1 inhomogeneity and resonance offsets can be effectively implemented using adiabatic heteronuclear dipolar recoupling pulse schemes. TEDOR-based 15N-13C and 15N-13C-13C chemical shift correlation experiments were carried out for obtaining 13C and 15N resonance assignments of an RNA composed of 97 (CUG) repeats which has been implicated in the neuromuscular disease myotonic dystrophy.     

Mathematical treatment of adiabatic fast passage pulses for the computation of nuclear spin relaxation rates in proteins with conformational exchange

Although originally designed for broadband inversion and decoupling in NMR spectroscopy, recent methodological developments have introduced adiabatic fast passage (AFP) pulses into the field of protein dynamics. AFP pulses employ a frequency sweep, and have not only superior inversion properties with respect to offset effects, but they are also easily implemented into a pulse sequence. As magnetization is dragged from the +z to the -z direction, Larmor precession is impeded since magnetization becomes spin-locked, which is a potentially useful feature for the investigation of microsecond to millisecond dynamics. A major drawback of these pulses as theoretical prediction is concerned, however, results from their time-dependent offset: simulations of spin density matrices under the influence of a time-dependent Hamiltonian with non-commuting elements are costly in terms of computational time, rendering data analysis impracticable. In this paper we suggest several ways to reduce the computational time without compromising accuracy with respect to effects such as cross-correlated relaxation and modulation of the chemical shift.     

Configurational analysis by residual dipolar couplings: A critical assessment of diastereomeric differentiabilities

Two independent statistical models for evaluating the certainties of configurational assignments of compounds based on nuclear magnetic resonance (NMR) data are evaluated and compared. Both methods yield weights or probabilities with which two or more structure models (constitutional or configurational isomers or even conformers) could be differentiated based on experimental parameters. Although this paper focusses on the use of residual dipolar couplings (RDCs) for the differentiation of diastereomers, the concept can be expanded to any set of experimental NMR‐derived parameters. It is demonstrated that highly reliable configurational assignments crucially must depend on thorough statistical analysis, which is frequently neglected in the literature.     

Robust refocusing of 13C magnetization in multidimensional NMR experiments by adiabatic fast passage pulses

We show that adiabatic fast passage (AFP) pulses are robust refocusing elements of transverse ¹³C magnetization in multidimensional NMR experiments. A pair of identical AFP pulses can refocus selected parts or a complete ¹³ C chemical shift range in ¹³C spectra. In the constant time ¹³C-¹H HSQC, replacement of attenuated rectangular pulses by selective AFP pulses results in a sensitivity enhancement of up to a factor of 1.8. In the 3D CBCA(CO)NH the signal-to-noise ratio is increased by a factor of up to 1.6.     

Solid state NMR at high magic angle spinning frequencies: Dipolar chemical shift correlation with adiabatic inversion pulse based RF pulse schemes

The efficacy of hetero- and homonuclear dipolar recoupling employing tanh/tan adiabatic inversion pulse based RF pulse schemes has been examined at high magic angle spinning (MAS) frequencies via numerical simulations and experimental measurements. An approach for minimising the recoupling RF power level is presented, taking into consideration the spinning speed, the range of resonance offsets and H₁ inhomogeneities and the available RF field strength. This involves the tailoring of the frequency and amplitude modulation profiles of the inversion pulses. The applicability of tanh/tan pulse based dipolar recoupling schemes to spinning speed regimes where the performance with conventional rectangular pulses may not be satisfactory is demonstrated.     

Mouse rump-white mutation associated with an inversion of Chromosome 5

The rump-white (Rw) mutation in the mouse was previously mapped as part of a cluster of spotting genes on Chromosome (Chr) 5 that includes the dominant spotting (W) and patch (Ph) loci. Recent studies have shown that the W locus encodes the KIT tyrosine kinase cell surface receptor and that Ph is a deletional mutation encompassing the platelet-derived growth factor receptor alpha subunit (Pdgfra) gene. However, the molecular basis of the Rw mutation remains to be established. We have analyzed an interspecific Mus spretus backcross segregating Rw and several loci proximal and distal to the W/Ph/Rw region to study the basis of this mutation. These studies indicated that loci within the En2 to Kit region of the chromosome do not recombine with one another even though they have been separated in other mapping studies presented here and elsewhere. We conducted a series of fluorescent in situ hybridization (FISH) studies with genomic probes to En2, Msx1, D5Buc1, and Kit to compare the physical order of these loci on the Rw and wild-type chromosomes. The Kit locus mapped to approximately the same region on both chromosomes of the Rw heterozygotes, while the positions of En2, Msx1, and D5Buc1 were reversed on the two chromosomes. Taken together, both the genetic and physical mapping data establish that the Rw mutation is associated with an inversion involving loci in the proximal region of Chromosome 5.     

siRecords: an extensive database of mammalian siRNAs with efficacy ratings

Short interfering RNAs (siRNAs) have been gaining popularity as the gene knock-down tool of choice by many researchers because of the clean nature of their workings as well as the technical simplicity and cost efficiency in their applications. We have constructed siRecords, a database of siRNAs experimentally tested by researchers with consistent efficacy ratings. This database will help siRNA researchers develop more reliable siRNA design rules; in the mean time, siRecords will benefit experimental researchers directly by providing them with information about the siRNAs that have been experimentally tested against the genes of their interest. Currently, more than 4100 carefully annotated siRNA sequences obtained from more than 1200 published siRNA studies are hosted in siRecords. This database will continue to expand as more experimentally tested siRNAs are published. Availability: The siRecords database can be accessed at http://siRecords.umn.edu/siRecords/     

A clinico-laboratory assessment of the efficacy of an Augmentin suspension in treating children with suppurative-inflammatory diseases caused by opportunistic bacteria]

Augmentin suspension (amoxycillin+clavulanic acid) was estimated in clinico-laboratory studies with respect to children suffering from pyoinflammatory diseases of various localization and its high efficacy was shown. Good and satisfactory results were recorded in 96.3 per cent of the cases in the treatment (monotherapy) and afterwards in the patients, adverse reactions such as nausea and vomiting being recorded only in 1 patient. The therapy with augmentin led to normalization of the microflora of the upper respiratory tract mucosa and a 1.5-fold increase in the neutrophil engulfment index.     

Sequence differentiation associated with an inversion on the neo-X chromosome of Drosophila americana

Sex chromosomes originate from pairs of autosomes that acquire controlling genes in the sex-determining cascade. Universal mechanisms apparently influence the evolution of sex chromosomes, because this chromosomal pair is characteristically heteromorphic in a broad range of organisms. To examine the pattern of initial differentiation between sex chromosomes, sequence analyses were performed on a pair of newly formed sex chromosomes in Drosophila americana. This species has neo-sex chromosomes as a result of a centromeric fusion between the X chromosome and an autosome. Sequences were analyzed from the Alcohol dehydrogenase (Adh), big brain (bib), and timeless (tim) gene regions, which represent separate positions along this pair of neo-sex chromosomes. In the northwestern range of the species, the bib and Adh regions exhibit significant sequence differentiation for neo-X chromosomes relative to neo-Y chromosomes from the same geographic region and other chromosomal populations of D. americana. Furthermore, a nucleotide site defining a common haplotype in bib is shown to be associated with a paracentric inversion [In(4)ab] on the neo-X chromosome, and this inversion suppresses recombination between neo-X and neo-Y chromosomes. These observations are consistent with the inversion acting as a recombination modifier that suppresses exchange between these neo-sex chromosomes, as predicted by models of sex chromosome evolution.     

Quantitative assessment of the germicidal efficacy of ultrasonic energy

Propagated (free-field) ultrasonic energy at a frequency of 26 kHz was used to expose aqueous suspensions of bacteria (Escherichia coli, Staphylococcus aureus, Bacillus subtilis, and Pseudomonas aeruginosa), fungus (Trichophyton mentagrophytes), and viruses (feline herpesvirus type 1 and feline calicivirus) to evaluate the germicidal efficacy of ultrasound. There was a significant effect of time for all four bacteria, with percent killed increasing with increased duration of exposure, and a significant effect of intensity for all bacteria except E. coli, with percent killed increasing with increased intensity level. There was a significant reduction in fungal growth compared with that in the controls, with decreased growth with increased ultrasound intensity. There was a significant reduction for feline herpesvirus with intensity, but there was no apparent effect of ultrasound on feline calicivirus. These results suggest that ultrasound in the low-kilohertz frequency range is capable to some degree of inactivating certain disease agents that may reside in water. The physical mechanism of inactivation appears to be transient cavitation.     

The assessment of antimalarial drug efficacy

Antimalarial drug efficacy in uncomplicated malaria should be assessed parasitologically in large, community-based trials, enrolling the age groups most affected by clinical disease. For rapidly eliminated drugs, a 28-day follow-up is needed, but, for slowly eliminated drugs, up to nine weeks could be required to document all recrudescences, and, when possible, the drug levels should also be measured. The WHO 14-day assessments are neither sensitive nor specific. In tropical Plasmodium vivax and Plasmodium ovale infections treated with chloroquine, the first relapse is usually suppressed by residual drug levels. A relapse cannot be distinguished confidently from a recrudescence. Host immunity is a major contributor to the therapeutic response, and can make failing drugs appear effective.     

Size of the pores created by an electric pulse: Microsecond vs millisecond pulses

Here, the sizes of the pores created by square-wave electric pulses with the duration of 100μs and 2ms are compared for pulses with the amplitudes close to the threshold of electroporation. Experiments were carried out with three types of cells: mouse hepatoma MH-22A cells, Chinese hamster ovary (CHO) cells, and human erythrocytes. In the case of a short pulse (square-wave with the duration of 100μs or exponential with the time constant of 22μs), in the large portion (30-60%) of electroporated (permeable to potassium ions) cells, an electric pulse created only the pores, which were smaller than the molecule of bleomycin (molecular mass of 1450Da, r≈0.8nm) or sucrose (molecular mass of 342.3Da, radius-0.44-0.52nm). In the case of a long 2-ms duration pulse, in almost all cells, which were electroporated, there were the pores larger than the molecules of bleomycin and/or sucrose. Kinetics of pore resealing depended on the pulse duration and was faster after the shorter pulse. After a short 100-μs duration pulse, the disappearance of the pores permeable to bleomycin was completed after 6-7min at 24-26°C, while after a long 2-ms duration pulse, this process was slower and lasted 15-20min. Thus, it can be concluded that a short 100-μs duration pulse created smaller pores than the longer 2-ms duration pulse. This could be attributed to the time inadequacy for pores to grow and expand during the pulse, in the case of short pulses.     

Local adaptation along an environmental cline in a species with an inversion polymorphism

Polymorphic inversions are ubiquitous across the animal kingdom and are frequently associated with clines in inversion frequencies across environmental gradients. Such clines are thought to result from selection favouring local adaptation; however, empirical tests are scarce. The seaweed fly Coelopa frigida has an α/β inversion polymorphism, and previous work demonstrated that the α inversion frequency declines from the North Sea to the Baltic Sea and is correlated with changes in tidal range, salinity, algal composition and wrackbed stability. Here, we explicitly test the hypothesis that populations of C. frigida along this cline are locally adapted by conducting a reciprocal transplant experiment of four populations along this cline to quantify survival. We found that survival varied significantly across treatments and detected a significant Location x Substrate interaction, indicating local adaptation. Survival models showed that flies from locations at both extremes had highest survival on their native substrates, demonstrating that local adaptation is present at the extremes of the cline. Survival at the two intermediate locations was, however, not elevated at the native substrates, suggesting that gene flow in intermediate habitats may override selection. Together, our results support the notion that population extremes of species with polymorphic inversions are often locally adapted, even when spatially close, consistent with the growing view that inversions can have direct and strong effects on the fitness of species.