Phage display peptide libraries: deviations from randomness and correctives

Peptide-expressing phage display libraries are widely used for the interrogation of antibodies. Affinity selected peptides are then analyzed to discover epitope mimetics, or are subjected to computational algorithms for epitope prediction. A critical assumption for these applications is the random representation of amino acids in the initial naïve peptide library. In a previous study, we implemented next generation sequencing to evaluate a naïve library and discovered severe deviations from randomness in UAG codon over-representation as well as in high G phosphoramidite abundance causing amino acid distribution biases. In this study, we demonstrate that the UAG over-representation can be attributed to the burden imposed on the phage upon the assembly of the recombinant Protein 8 subunits. This was corrected by constructing the libraries using supE44-containing bacteria which suppress the UAG driven abortive termination. We also demonstrate that the overabundance of G stems from variant synthesis-efficiency and can be corrected using compensating oligonucleotide-mixtures calibrated by mass spectroscopy. Construction of libraries implementing these correctives results in markedly improved libraries that display random distribution of amino acids, thus ensuring that enriched peptides obtained in biopanning represent a genuine selection event, a fundamental assumption for phage display applications.

Saddle antenna radio frequency ion sources

Existing RF ion sources for accelerators have specific efficiencies for H(+) and H(-) ion generation ∼3-5 mA/cm(2) kW, where about 50 kW of RF power is typically needed for 50 mA beam current production. The Saddle Antenna (SA) surface plasma source (SPS) described here was developed to improve H(-) ion production efficiency, reliability, and availability. In SA RF ion source, the efficiency of positive ion generation in the plasma has been improved to 200 mA/cm(2) kW. After cesiation, the current of negative ions to the collector was increased from 1 mA to 10 mA with RF power ∼1.5 kW in the plasma (6 mm diameter emission aperture) and up to 30 mA with ∼4 kW RF. Continuous wave (CW) operation of the SA SPS has been tested on the test stand. The general design of the CW SA SPS is based on the pulsed version. Some modifications were made to improve the cooling and cesiation stability. CW operation with negative ion extraction was tested with RF power up to ∼1.2 kW in the plasma with production up to Ic = 7 mA. A stable long time generation of H(-) beam without degradation was demonstrated in RF discharge with AlN discharge chamber.

Characterization of the CW starter plasma RF matching network for operating the SNS H⁻ ion source with lower H₂ flows

The Spallation Neutron Source H(-) ion source is operated with a pulsed 2-MHz RF (50-60 kW) to produce the 1-ms long, ∼50 mA H(-) beams at 60 Hz. A continuous low power (∼300 W) 13.56-MHz RF plasma, which is initially ignited with a H2 pressure bump, serves as starter plasma for the pulsed high power 2-MHz RF discharges. To reduce the risk of plasma outages at lower H2 flow rates which is desired for improved performance of the following radio frequency quadrupole, the 13.56-MHz RF matching network was characterized over a broad range of its two tuning capacitors. The H-α line intensity of the 13.56-MHz RF plasma and the reflected power of the 13.56-MHz RF were mapped against the capacitor settings. Optimal tunes for the maximum H-α intensity are consistent with the optimal tunes for minimum reflected power. Low limits of the H2 flow rate not causing plasma outages were explored within the range of the map. A tune region that allows lower H2 flow rate has been identified, which differs from the optimal tune for global minimum reflected power that was mostly used in the past.

The status of the SNS external antenna ion source and spare RFQ test facility

The Oak Ridge National Laboratory operates the Spallation Neutron Source, consisting of a H(-) ion source, a 1 GeV linac and an accumulator ring. The accumulated <1 μs-long, ∼35 A beam pulses are extracted from the ring at 60 Hz and directed onto a liquid Hg target. Spalled neutrons are directed to ∼20 world class instruments. Currently, the facility operates routinely with ∼1.2 MW of average beam power, which soon will be raised to 1.4 MW. A future upgrade with a second target station calls for raising the power to 2.8 MW. This paper describes the status of two accelerator components expected to play important roles in achieving these goals: a recently acquired RFQ accelerator and the external antenna ion source. Currently, the RFQ is being conditioned in a newly constructed 2.5 MeV Integrated Test Facility (ITF) and the external antenna source is also being tested on a separate test stand. This paper presents the results of experiments and the testing of these systems.

Recent performance of and plasma outage studies with the SNS H⁻ source

Spallation Neutron Source ramps to higher power levels that can be sustained with high availability. The goal is 1.4 MW despite a compromised radio frequency quadrupole (RFQ), which requires higher radio frequency power than design levels to approach the nominal beam transmission. Unfortunately at higher power the RFQ often loses its thermal stability, a problem apparently enhanced by beam losses and high influxes of hydrogen. Delivering as much H(-) beam as possible with the least amount of hydrogen led to plasma outages. The root cause is the dense 1-ms long ∼55-kW 2-MHz plasma pulses reflecting ∼90% of the continuous ∼300 W, 13-MHz power, which was mitigated with a 4-ms filter for the reflected power signal and an outage resistant, slightly detuned 13-MHz match. Lowering the H2 gas also increased the H(-) beam current to ∼55 mA and increased the RFQ transmission by ∼7% (relative).

Improving efficiency of negative ion production in ion source with saddle antenna

Extraction of negative ions from a saddle antenna radio-frequency surface plasma source is considered. Several versions of new plasma generators with different antennas and magnetic field configurations were tested in the smal Oak Ridge National Laboratory Spallation Neutron Source Test Stand. The efficiency of positive ion generation in plasma has been improved to 200 mA/cm(2) kW from 2.5 mA/cm(2) kW. A small oven was developed for cesiation by cesium compounds and alloy decomposition. After cesiation, a current of negative ions to the collector was increased from 1 mA to 10 mA with 1.5 kW RF power in the plasma and longitudinal magnetic field Bl ∼ 250 G. The specific efficiency of H(-) production was increased to 20 mA/cm(2) kW from 2.5 mA/cm(2) kW.

Recent performance of the SNS H(-) ion source and low-energy beam transport system

Recent measurements of the H(-) beam current show that SNS is injecting about 55 mA into the RFQ compared to ∼45 mA in 2010. Since 2010, the H(-) beam exiting the RFQ dropped from ∼40 mA to ∼34 mA, which is sufficient for 1 MW of beam power. To minimize the impact of the RFQ degradation, the service cycle of the best performing source was extended to 6 weeks. The only degradation is fluctuations in the electron dump voltage towards the end of some service cycles, a problem that is being investigated. Very recently, the RFQ was retuned, which partly restored its transmission. In addition, the electrostatic low-energy beam transport system was reengineered to double its heat sinking and equipped with a thermocouple that monitors the temperature of the ground electrode between the two Einzel lenses. The recorded data show that emissions from the source at high voltage dominate the heat load. Emissions from the partly Cs-covered first lens cause the temperature to peak several hours after starting up. On rare occasions, the temperature can also peak due to corona discharges between the center ground electrode and one of the lenses.

Surface plasma source with saddle antenna radio frequency plasma generator

A prototype RF H(-) surface plasma source (SPS) with saddle (SA) RF antenna is developed which will provide better power efficiency for high pulsed and average current, higher brightness with longer lifetime and higher reliability. Several versions of new plasma generators with small AlN discharge chambers and different antennas and magnetic field configurations were tested in the plasma source test stand. A prototype SA SPS was installed in the Spallation Neutron Source (SNS) ion source test stand with a larger, normal-sized SNS AlN chamber that achieved unanalyzed peak currents of up to 67 mA with an apparent efficiency up to 1.6 mA∕kW. Control experiments with H(-) beam produced by SNS SPS with internal and external antennas were conducted. A new version of the RF triggering plasma gun has been designed. A saddle antenna SPS with water cooling is fabricated for high duty factor testing.

Producing persistent, high-current, high-duty-factor H- beams for routine 1 MW operation of Spallation Neutron Source (invited)

Since 2009, the Spallation Neutron Source (SNS) has been producing neutrons with ion beam powers near 1 MW, which requires the extraction of ∼50 mA H(-) ions from the ion source with a ∼5% duty factor. The 50 mA are achieved after an initial dose of ∼3 mg of Cs and heating the Cs collar to ∼170 °C. The 50 mA normally persist for the entire 4-week source service cycles. Fundamental processes are reviewed to elucidate the persistence of the SNS H(-) beams without a steady feed of Cs and why the Cs collar temperature may have to be kept near 170 °C.

Effect of opioid active therapeutics on the ascending reflex pathway in the rat ileum

For a long time therapeutic agents that interact with opioid receptors have been used in antidiarrheal therapy. The action of the opioid active substances on motility and transit have already been characterized; however, their effects on myenteric reflexes and their possible luminal action have not yet been investigated. Loperamide, fedotozine and beta-casomorphin-4, as well as the casomorphin-analogue beta-CM-4027, are, or have been, suggested as therapeutic agents and were studied in the isolated rat ileum for their effect on the ascending reflex pathway. beta-CM-4027 > fedotozine > loperamide > beta-casomorphin-4 caused a concentration-dependent inhibition of the ascending contractile reflex response with an IC(50)of 1.4x10(-7)M, 1.5x10(-6)M, 4.1x10(-6)M and 4.5x10(-6)M respectively. At the same time as the oral contractile reflex response was inhibited, all four opioid agonists (CM-4027 > beta-casomorphin-4 > fedotozine > loperamide) increased the latency of the reflex response. Both effects were blocked by naloxone, indicating the involvement of opioid receptors. These results demonstrate that opioid-active drugs and substances modify the peristaltic reflex by reducing the efficacy of the reflex response and modulating the timing of the reflex pathway. In a second series of experiments, luminal application of opioid-active drugs was compared with serosal application. beta-casomorphine-4 caused a concentration-dependent inhibition of the oral reflex response with an IC(50)of 3x10(-3)M which was 750 times higher than after serosal application. In contrast, a stable and highly selective kappa opioid agonist (U-50,488), which caused potent inhibition upon serosal application (IC(50): 2.3x10(-7)M), showed no inhibitory effect after luminal application up to a concentration of 10(-2)M. Thus casomorphins could have a local effect on the gut wall with no need for systemic absorption. This might be used for a possible therapeutic application.

Ascending neural pathways in the rat ileum in vitro — Effect of capsaicin and involvement of nitric oxide

The aim of the present study was to develop and characterize an in vitro model of the rat ileum in which activation of the orally projecting neural excitatory pathway of the myenteric reflex is produced by electrical field stimulation anally to the recording site. The motility of a 10-cm segment of rat ileum was recorded using a perfused manometric assembly with side holes 2 and 4 cm orally to the stimulation site. Electrical field stimulation caused a contractile response in the oral but not in the aboral direction of the stimulation site. The contractile response, which was maximal using low stimulus frequencies (3 or 5 pulses per second (pps)) and decreased with higher frequencies (10 or 20 pps), was blocked by atropine (10(-6) M) at all frequencies tested after acute and after prolonged (greater than 30 min) treatment. The maximal contractile response at 3 pps was abolished by hexamethonium (10(-4) M), tetrodotoxin (5 x 10(-7) M) and by complete transection of the muscular wall between the stimulation and the recording site. Acute administration of capsaicin (8 x 10(-7) M) to the bath reduced the lag between the start of the electrical stimulation and the onset of the contractile response. Higher concentrations of capsaicin (10(-5) M) reduced the contractile response, but this was partly due to an unspecific effect of capsaicin. Blockade of nitric oxide (NO) synthesis by L-NG-nitro-arginine-methyl ester (L-NAME) (3 x 10(-4) M) augmented the contractile response to anal stimulation by 222.4% and reduced the lag period by 54.5%, whereas the stereoisomer D-NAME had no significant effect. The potentiating effects of L-NAME were reversed in the presence of L-arginine (3 x 10(-3) M) but not in the presence of the stereoisomer D-arginine (3 x 10(-3) M). This model can be used to study ascending neural pathways in the rat small intestine. The ascending excitatory response is abolished by atropine and hexamethonium and is modulated by capsicin-sensitive fibers. The ascending pathway is under tonic inhibition of metabolites of the L-arginine-NO pathway.