David Taggart

Human DNA Polymerase ϵ Is Able to Efficiently Extend from Multiple Consecutive Ribonucleotides

Background: Ribonucleotides in DNA are associated with genome instability. Results: Human DNA polymerase ϵ catalyzes efficient incorporation of ribonucleotides and extension from primers terminating in multiple consecutive ribonucleotides. Conclusion: Human DNA polymerase ϵ is able to extend ribonucleotide-terminal primers through a reduction in its proofreading activity. Significance: Leading strand replication may have a unique relationship to ribonucleotides, RNA, and genome stability. Replicative DNA polymerases (Pols) help to maintain the high fidelity of replication in large part through their strong selectivity against mispaired deoxyribonucleotides. It has recently been demonstrated that several replicative Pols from yeast have surprisingly low selectivity for deoxyribonucleotides over their analogous ribonucleotides. In human cells, ribonucleotides are found in great abundance over deoxyribonucleotides, raising the possibility that ribonucleotides are incorporated in the human genome at significant levels during normal cellular functions. To address this possibility, the ability of human DNA polymerase ϵ to incorporate ribonucleotides was tested. At physiological concentrations of nucleotides, human Pol ϵ readily inserts and extends from incorporated ribonucleotides. Almost half of inserted ribonucleotides escape proofreading by 3′ → 5′ exonuclease-proficient Pol ϵ, indicating that ribonucleotide incorporation by Pol ϵ is likely a significant event in human cells. Human Pol ϵ is also efficient at extending from primers terminating in up to five consecutive ribonucleotides. This efficient extension appears to result from reduced exonuclease activity on primers containing consecutive 3′-terminal ribonucleotides. These biochemical properties suggest that Pol ϵ is a likely source of ribonucleotides in human genomic DNA.

Wideband gapfiller satellite (WGS) system

The wideband gapfiller satellites will provide near-term continuation and augmentation of the services currently provided by the defense satellite communications system (DSCS) and the global broadcast service (GBS) Ka services currently provided by GBS payloads on UFO satellites. WGS will provide services to the U.S. Department of Defense and other Government users. The Gapfiller satellites will serve as a means to continue and increase the capability of wideband services between the period of approximately 2005 to 2025. This paper presents (1) a review of some of the important features of the WGS system and (2) key design issues for the flexible digital channelizer, which is critical to the routing and switching performed on-board the satellite. The results contained in this submission were generated in whole, or in part, through work supporting the MILSATCOM joint program office (MJPO). The authors are very appreciative of the insight provided by the SMC/MC program office of the Space and Missile Center and Boeing Satellite Systems (BSS) in understanding portions of the wideband gapfiller satellite

Quantitative analysis of the mutagenic potential of 1-aminopyrene-DNA adduct bypass catalyzed by Y-family DNA polymerases

N-(Deoxyguanosin-8-yl)-1-aminopyrene (dG(AP)) is the predominant nitro polyaromatic hydrocarbon product generated from the air pollutant 1-nitropyrene reacting with DNA. Previous studies have shown that dG(AP) induces genetic mutations in bacterial and mammalian cells. One potential source of these mutations is the error-prone bypass of dG(AP) lesions catalyzed by the low-fidelity Y-family DNA polymerases. To provide a comparative analysis of the mutagenic potential of the translesion DNA synthesis (TLS) of dG(AP), we employed short oligonucleotide sequencing assays (SOSAs) with the model Y-family DNA polymerase from Sulfolobus solfataricus, DNA Polymerase IV (Dpo4), and the human Y-family DNA polymerases eta (hPolη), kappa (hPolκ), and iota (hPolι). Relative to undamaged DNA, all four enzymes generated far more mutations (base deletions, insertions, and substitutions) with a DNA template containing a site-specifically placed dG(AP). Opposite dG(AP) and at an immediate downstream template position, the most frequent mutations made by the three human enzymes were base deletions and the most frequent base substitutions were dAs for all enzymes. Based on the SOSA data, Dpo4 was the least error-prone Y-family DNA polymerase among the four enzymes during the TLS of dG(AP). Among the three human Y-family enzymes, hPolκ made the fewest mutations at all template positions except opposite the lesion site. hPolκ was significantly less error-prone than hPolι and hPolη during the extension of dG(AP) bypass products. Interestingly, the most frequent mutations created by hPolι at all template positions were base deletions. Although hRev1, the fourth human Y-family enzyme, could not extend dG(AP) bypass products in our standing start assays, it preferentially incorporated dCTP opposite the bulky lesion. Collectively, these mutagenic profiles suggest that hPolk and hRev1 are the most suitable human Y-family DNA polymerases to perform TLS of dG(AP) in humans.

Simulation and modeling of amplifier nonlinearities for multicarrier wireless communication systems

Amplifier nonlinearities impact the performance of multicarrier frequency division multiple access (FDMA) wireless communication systems. It is important to accurately model limiters and high power amplifiers to predict the bit error rate performance of multicarrier communication systems. Modern simulation tools can be used to accurately determine intermodulation distortion and its effect on the bit error rate in a computationally timely manner. This paper presents simulation results in a parameterized form when the input to the amplifier is comprised of a number of 8-PSK modulated signals with raised cosine filter shaping. One of the important parameter in these simulated results is the amplifier power back off level, which is varied over a range of about 6 dB. The simulation results include the probability of bit error and the intermodulation distortion both within the signal band and outside the signal band. Bit error rate curves, eye diagrams and constellation figures are used in presenting the results.

ANALOG-TO-DIGITAL CONVERTERS LOAD FACTOR ANALYSIS FOR WIDEBAND COMMUNICATION SATELLITE SYSTEMS

In modern satellites systems the uplink RF wideband signal after downconversion to IF is input to the analogto-digital converter, the output of which is digitally processed for the purpose of channelization and switching of signals. In such systems, a major implementation limitation is the A/D converter, which needs to operate at a rate at least two times the received wideband signal bandwidth. In the case of a wideband signal comprised of many multiplexed signals, the spectral distribution of quantization noise is also of significant interest. Another very important consideration in the ADC performance analysis is the signal clipping effect occurring whenever the instantaneous input signal amplitude exceeds the maximum linear range of the quantizer. Since clipping cannot be avoided in most practical situations, the signal power to the quantization plus clipping noise power ratio is of utmost interest. Such a ratio is in general a function of the quantizer load factor that in turn is the ratio of the input signal average power and the maximum peak power at the quantizer output. The paper presents simulation results on the quantizer load factor analysis when the input signal is comprised of a specified number of digitally modulated carriers. As simulation examples, 8-PSK and 16-QAM modulation schemes are considered with and without band limiting filtering.

Communication system performance - detailed modeling of a power amplifier with two modulated input signals

The performance of multicarrier frequency division multiple access (FDMA) wireless communication systems is impacted by amplifier nonlinearities. It is vital to precisely model limiters and high power amplifiers (HPAs) to determine the spectrum distortion and other types of degradation associated with multicarrier communication systems. Contemporary simulation tools can be employed to precisely ascertain intermodulation (IM) distortion and its effect and impact on both in-band and out-of-band IM performance in a computationally timely manner. This paper illustrates analysis and simulation results in a parameterized form when the amplifier input consists of two 8-PSK modulated signals with raised cosine filter shaping. One of the significant parameters in these analyses and simulated results is the HPA operational back-off (OBO) power level, which is studied over a range of about 6 dB. The simulation illustrates the intermodulation distortion both within the signal band and outside the signal band. A novel approach is used to represent an HPA in terms of a power series expansion, which converges very rapidly and gives significant insight and provides a useful tool in predicting the spectral content of the HPA output. The results contained in this submission were generated in whole, or in part, through work supporting the MILSATCOM joint program office (MJPO). The authors are very appreciative of the support provided by the SMC/MC program office of the Space and Missile Center in this effort

Mutagenic potential of 8-oxo-7,8-dihydro-2'-deoxyguanosine bypass catalyzed by human Y-family DNA polymerases.

One of the most common lesions induced by oxidative DNA damage is 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG). Replicative DNA polymerases poorly traverse this highly mutagenic lesion, suggesting that the replication fork may switch to a polymerase specialized for translesion DNA synthesis (TLS) to catalyze 8-oxodG bypass in vivo. Here, we systematically compared the 8-oxodG bypass efficiencies and fidelities of the TLS-specialized, human Y-family DNA polymerases eta (hPolη), iota (hPolι), kappa (hPolκ), and Rev1 (hRev1) either alone or in combination. Primer extension assays revealed that the times required for hPolη, hRev1, hPolκ, and hPolι to bypass 50% of the 8-oxodG lesions encountered (t50bypass) were 0.58, 0.86, 108, and 670 s, respectively. Although hRev1 bypassed 8-oxodG efficiently, hRev1 failed to catalyze the extension step of TLS, and a second polymerase was required to extend the lesion bypass products. A high-throughput short oligonucleotide sequencing assay (HT-SOSA) was used to quantify the types and frequencies of incorporation errors produced by the human Y-family DNA polymerases at and near the 8-oxodG site. Although hPolη bypassed 8-oxodG most efficiently, hPolη correctly incorporated dCTP opposite 8-oxodG within only 54.5% of the sequences analyzed. In contrast, hPolι bypassed the lesion least efficiently but correctly incorporated dCTP at a frequency of 65.8% opposite the lesion. The combination of hRev1 and hPolκ was most accurate opposite 8-oxodG (92.3%), whereas hPolκ alone was the least accurate (18.5%). The t50bypass value and correct dCTP incorporation frequency in the presence of an equal molar concentration of all four Y-family enzymes were 0.60 s and 43.5%, respectively. These values are most similar to those of hPolη alone, suggesting that hPolη outcompetes the other three Y-family polymerases to catalyze 8-oxodG bypass in vitro and possibly in vivo.

Analog-to-Digital Converter Loading Analysis Considerations for Satellite Communications Systems

In contemporary communication satellite systems, uplink radio frequency (RF) signals are amplified, downconverted to intermediate frequency (IF) and/or baseband, and after appropriate filtering, are input to an analog-to-digital converter (ADC). The ADC digital output is signal processed for a variety of purposes, such as signal channelization and switching. In these systems, a foremost realization problem is the ADC, which must operate to satisfy the sampling theorem, which necessitates a sampling rate at least twice the received signal bandwidth. When the signal consists of numerous multiplexed signals, a critical matter in ADC performance is the degree of signal clipping, which arises when the instantaneous ADC input signal magnitude surpasses the maximum range of the ADC. Since at least some clipping is often present, the total ADC noise output consists of clipping plus quantization noise. A figure of merit for the ADC is the signal-to-noise ratio (SNR) of the ADC, which is defined as the ratio of input signal average power to the ADC output average noise power. The SNR is determined by, among other things, the ADC load factor, which is the ratio of the ADC input signal average power, and the ADC maximum peak power output. This paper describes analysis and simulation results on SNR versus the ADC load factor when the input signal is composed of many digitally modulated carriers. A nine-signal 8-ary phase shift key (8-PSK) modulated carrier case is considered with each signal band limited. It is important to note that for this particular ADC input, it is shown that the probability density function (PDF) is Gaussian-like. This is significant since this means that the SNR versus ADC load factor curve for the nine 8-PSK signal case will have nearly identical characteristics to that when the ADC input is white Gaussian noise. Additionally, this paper discusses what occurs when the ADC is strongly driven into the clipping region. This discussion is enhanced by comparing the ADC to a limiter in this highly distorted region. Analysis and simulation results are provided to describe ADC performance characteristics in this highly distorted region.

Probability of error analysis of analog-to-digital converters with multiple 8-PSK modulated signals

In modern satellite systems the uplink RF wideband signal after down conversion to IF is input to the analog-to-digital converter (ADC), the output of which is digitally processed for the purpose of channelization and switching of signals. In such systems, a major implementation limitation is the ADC, which needs to operate at a rate at least two times the received signal bandwidth. In the case of a wideband signal composed of many multiplexed signals, the spectral distribution of quantization noise is also of significant interest. Another very important consideration in the ADC performance analysis is the signal clipping effect that occurs whenever the instantaneous input signal amplitude exceeds the maximum linear range of the quantizer. Since clipping cannot be avoided in most practical situations, the signal power to the quantization- plus- clipping- noise-power ratio is of utmost interest. Such a ratio is in general a function of the quantizer load factor that in turn is the ratio of the input signal average power to the maximum peak power at the quantizer output. Even more important for digital communication is the probability of symbol error obtained in the presence of quantization and clipping noise in addition to the receiver thermal noise. The paper presents simulation results on the quantizer analysis when the input signal is composed of a specified number of 8-PSK modulated signals, which have been band limited by square root raised cosine filters. The results are obtained in terms of the probability of symbol error as a function of quantizer load factor

Performance of MPSK and 16QAM in the satellite communication environment

This paper presents computer simulation results on the performance of quadrature phase shift keying (QPSK), 8-ary phase shift keying (8PSK), and 16 quadrature amplitude modulation (16QAM) schemes in a satellite communication environment employing frequency division multiple accessing (FDMA). The end-to-end communication system, which includes the modulator, klystron amplifier, satellite transponder, carrier and timing recovery loops, and the channel filters, is modeled using the cadence signal processing work system (SPW) tool. The satellite transponder components modeled in SPW include filters, up/down converters, digital channelizer filters, and high-power amplifiers (HPAs). Measured data is used to characterize the transmitter klystron and the transponder HPA. The performance of the filtered signal of interest is evaluated in the presence of filtered QPSK, 8PSK, and 16QAM signals in adjacent channels. Due to the complex waveforms, the nonlinear channel model, and the multi-user scenario involved in the simulations, it is very difficult to develop an analytical expression to accurately predict the received signal power level. Therefore, a power calibration process is developed to determine the received signal power level, required to compute the bit energy to noise spectral density ratio (E/sub b//N/sub o/) used in any specific SPW simulation run. Simulation results of the paper show that the bit error rate (BER) performance of the simulated communication system is significantly impacted by the presence of the adjacent channel interference (ACI) and the intermodulation (IM) noise.