Quasiparticle Poisoning of Superconducting Qubits from Resonant Absorption of Pair-Breaking Photons

The ideal superconductor provides a pristine environment for the delicate states of a quantum computer: because there is an energy gap to excitations, there are no spurious modes with which the qubits can interact, causing irreversible decay of the quantum state. As a practical matter, however, there exists a high density of excitations out of the superconducting ground state even at ultralow temperature; these are known as quasiparticles. Observed quasiparticle densities are of order 1  μm^{-3}, tens of orders of magnitude greater than the equilibrium density expected from theory. Nonequilibrium quasiparticles extract energy from the qubit mode and can induce dephasing. Here we show that a dominant mechanism for quasiparticle poisoning is direct absorption of high-energy photons at the qubit junction. We use a Josephson junction-based photon source to controllably dose qubit circuits with millimeter-wave radiation, and we use an interferometric quantum gate sequence to reconstruct the charge parity of the qubit. We find that the structure of the qubit itself acts as a resonant antenna for millimeter-wave radiation, providing an efficient path for photons to generate quasiparticles. A deep understanding of this physics will pave the way to realization of next-generation superconducting qubits that are robust against quasiparticle poisoning.

Oral Cavity Squamous Cell Carcinomas in Patients with a History of Oral Lichen Planus: Frequency and Outcomes

PURPOSE/OBJECTIVE(S)

Oral lichen planus (OLP) is an inflammatory condition which affects the mucous membranes of the oral cavity. While previous studies have described the association between OLP and development of oral cavity cancer, there is currently a paucity of literature examining the impact of this disease on treatment response and prognosis. As such, we present a retrospective cohort study of Oral cavity squamous cell carcinoma (OCSCC) patients with a history of OLP to explore the course of their disease.

MATERIALS/METHODS

Using an IRB approved tertiary care registry of head and neck cancer patients, we identified patients with OCSCC who had a prior diagnosis of OLP. The number of new primary tumors, rates of local (LF), regional (RF) and distant failure (DF), as well as overall survival (OS) were assessed using Cox proportional hazards and Kaplan Meier analysis for actuarial survival estimates.

RESULTS

Fifty-four patients with OCSCC and OLP were identified with 109 individual OCSCC diagnoses. Patients had a median age of 67 years, were predominantly female (n = 42, 77.8%) and never smokers (n = 29, 53.7%) with a median follow up after diagnosis of OCSCC of 46.5 months. Nine patients (16.7%) had a history of immunosuppression of whom 6 (11.1%) had chronic steroid use for treatment of OLP. Within the cohort, 33 (61.1%) of OLP patients had a single OCSCC, 11 (20.4%) had 2, and 10 (18.5%) had >3 separate tumors develop. The most common oral cavity subsites were oral tongue (n = 42, 38.5%), followed by alveolar ridge (n = 14, 12.8%) and gingiva (n = 13, 11.9%). Papillary SCC subtype was identified in 10.1%. 92.7% of tumors (n = 101) were treated with primary surgery, with 23 (21.1%) receiving adjuvant RT and 10 of those patients receiving concurrent chemotherapy. Among resected patients, pathologic stages were predominantly T1-2 (84.1%) and N0 (50% vs N1 15.6% and N2a-3 34.4%). The mean RT dose was 62 Gy in 32 fractions. Locoregional failure occurred in 24.8% of cancers (n = 27), with local and regional failure occurring in 13.8% (n = 15) and 11% (n = 12) of lesions, respectively. Recurrence free survival at 3 and 5 years was 75% and 70.3%, respectively, with overall survival at 3 and 5 years of 71.1% and 67%, respectively.

CONCLUSION

Patients with OCSCC and a history of OLP are predominantly female and never smokers. The tumors that develop in such patients are often early stage but a proportion of patients appear to be at higher risk of developing multiple malignancies and surveillance of this patient population to identify new tumors is crucial.

Definitive Radiotherapy for the Treatment of Gross Disease in Unresected Differentiated Thyroid Cancer

PURPOSE/OBJECTIVE(S)

While surgery (with or without radioactive iodine (RAI)) is the mainstay of locoregional control in differentiated thyroid cancer (DTC), patients with unresectable disease present a clinical challenge. Uncontrolled disease in the neck can lead to substantial morbidity and mortality in DTC and obtaining locoregional control is vital to preserving quality of life and longevity. High dose definitive radiotherapy (RT) for gross disease in DTC is understudied. This study examines the efficacy of definitive RT in this setting.

MATERIALS/METHODS

From an IRB-approved registry of head and neck cancer cases treated at a tertiary care center over a period of 8 years (2014-2022), patients with incompletely resected or unresectable DTC including papillary, follicular, mixed, medullary, and poorly differentiated types were identified. All patients were treated to the neck and/or thyroid regions with visible gross disease to a definitive dose of radiation. The primary endpoint was local control within the radiated portal with a secondary endpoint of locoregional control within the neck.

RESULTS

A total of 31 patients were identified, of whom 74.2% were Caucasian. Fourteen were female (45.2%), and 17 (54.8%) were male. The median age was 68 years (range 26-90) and the median follow-up was 31 months. Histologically, 19 (61.3%) cases were papillary, 4 (12.9%) were follicular, 2 (6.5%) were mixed, 3 (9.7%) were medullary, and 3 (9.7%) were poorly differentiated. Among patients with non-medullary DTC 18 (69.2%) received prior RAI. Twelve patients were treated with radiation at initial diagnosis, while 19 patients were treated at the time of recurrence; two patients received concurrent chemotherapy. Twenty-eight patients (90.3%) were treated with IMRT and 3 (9.7%) were treated with SBRT. The median dose to the gross disease was 66 Gy (range 30-70.4) in 32 fractions (range 5-35). Overall, 5 patients (16.1%) experienced a locoregional failure after RT and all experienced failure in the RT portal. The actuarial infield control/locoregional control of radiation therapy at 3 and 5 years was 84.8% and 74.2%, respectively. Overall survival at 3 and 5 years was 68.5% and 47.4%, respectively. Among patients who had a locoregional failure after RT, 2 patients were salvaged with systemic therapy, 2 patients with surgery, and 1 patient with SBRT re-irradiation (40 Gy/5 fractions). The patient salvaged with SBRT remains without disease 8 months post-RT.

CONCLUSION

Definitive radiotherapy is a highly effective strategy to obtain durable control of unresected DTC. It should be standard for unresected disease and considered as a viable alternative for patients with borderline resectable disease for whom resection would be highly morbid.

P02.01.B The telomere maintenance mechanism spectrum and its dynamics in gliomas

The activation of the telomere maintenance mechanism (TMM) is one of the critical drivers of cancer cell immortality. In gliomas, TERT expression and TERT promoter mutation are considered to reliably indicate telomerase activation, while ATRX mutation indicates alternative lengthening of telomeres (ALT). However, these relationships have not been extensively validated in tumor tissues. Here, we show through the direct measurement of telomerase activity and ALT in a large set of glioma samples that the TMM in glioma cannot be defined in the dichotomy of telomerase activity and ALT, regardless of TERT expression, TERT promoter mutation and ATRX mutation. Moreover, we observed that a considerable proportion of gliomas lack both telomerase activity and ALT (Neither group). And this Neither group exhibited evidence of slow growth potential. From a set of longitudinal samples from a separate cohort of glioma patients, we discovered that the TMM is not fixed but changes with glioma progression. Collectively, these results suggest that the TMM is a dynamic entity and that reflects the plasticity of the oncogenic biological status of tumor cells and that the TMM should be defined by the direct measurement of telomerase enzyme activity and evidence of ALT.

0791 Effects of Low Frequency Electrical Stimulators as Nonpharmacological Treatment in Restless Legs Syndrome

Introduction

Non-pharmacological treatments for restless legs syndrome (RLS) is a treatment option for patients who have not yet started medical treatment, who do not respond to their prescribed medication, or who suffer from adverse effects of medication. This study aims to investigate the clinical effectiveness of low frequency electronic stimulators (LFES) as a non-pharmacological treatment.

Methods

This is a randomized, single-blind study. After screening 64 patients according to the inclusion/exclusion criteria, a total of 46 patients participated in the study. The participants were separated into an active group and a sham group with 22 and 24 members, respectively. The stimulation was administered using the tapping mode (3Hz) present on the machines used, and symptom changes were measured in both groups. The effects of the stimuli were analyzed with repeated measures ANOVA.

Results

Symptom severity was significantly reduced in the active group, and showed significant interaction effects in the time multiple group. Although both the active and sham groups reported improved symptoms upon receiving longer periods of treatment, the effect of the LFES was greater in the active group.

Conclusion

Analyzing the effects of LFES by dividing the active and sham groups revealed that LFES treatment resulted in symptom improvement when using effective stimulation intensity. LFES can be a non-pharmacological treatment option for RLS.

Support

None

Variability of Faecal Calprotectin in Inflammatory Bowel Disease Patients: An Observational Case-control Study

BACKGROUND AND AIMS

Several factors have been reported to affect faecal calprotectin [FC] values, and significant variation in FC concentrations has been observed in inflammatory bowel disease [IBD] patients. We aimed to evaluate FC variability in IBD patients, and to assess the robustness of a single stool punch.

METHODS

This is a single-centre observational case-control study. Disease activity was assessed using endoscopic and clinical activity scores, as well as C-reactive protein levels. Stool samples were collected twice within a 1 to 6 days interval, and FC was measured on punches and homogenates by fluorometric enzyme immunocapture assay.

RESULTS

In all, 260 stool samples were collected from 120 patients. Intrastool variability was low, with an intraclass correlation coefficient for single measures between three punches from a single stool sample of 0.91, and median coefficient of variation [CV] of 17%. CV of two stool samples a few days apart [intra-individual variability] were significantly higher [p <0.01] with median CV of 36%. FC standard deviations correlated with mean FC levels either for intrastool or for intra-individual variability, with a Spearman's coefficient of rank correlation of 0.85 and 0.78, respectively [p <0.01]. Disease type, location, activity, and FC levels did not influence variability.

CONCLUSIONS

A single stool punch is reliable for FC measurement, considering that intrastool variability is low. Intra-individual variability a few days apart is significantly higher. Therefore, decision-making strategies based on single measurements should consider this variability, to determine the minimum optimal variation to be achieved, rather than a cut-off, especially in high FC levels.

Cryopreservation of Endangered Wild Species, Aster altaicus var. uchiyamae Kitam, Using Droplet-Vitrification Procedure

BACKGROUND

Aster altaicus var. uchiyamae Kitam is an endemic and endangered species in urgent need of a comprehensive conservation strategy.

OBJECTIVE

To develop an efficient cryopreservation protocol using in vitro shoot tips to complement traditional conservation approaches in case seeds are not available or insufficient for conservation programs.

METHODS

Shoot tips of in vitro plants were cryopreserved using a droplet-vitrification method following improvement of pre-culture, osmoprotection, vitrification solution (VS), unloading and post-culture treatments. The starting protocol included step-wise pre-culture with 10% and 17.5% sucrose for 55 h and 17 h, respectively, followed by osmoprotection with C4-35% (17.5% glycerol + 17.5% sucrose) for 30 min, and cryoprotection with B5-80% (40% glycerol + 40% sucrose) for 60 min.

RESULTS

Shoot tips of A. altaicus were found to be moderately sensitive to the osmotic stress. Pre-culture and osmoprotection were not critical for the regeneration of cryopreserved explants when either of these treatments was applied. Osmoprotection with C4-35% on ice for 60 min followed by cryoprotection with A3-80%, a modified and diluted PVS2, on ice for 60 min resulted in the highest (65.3%) regeneration of cryopreserved shoot tips. Among alternative VSs tested, A3-80% and B5-80% were superior to PVS2 and PVS3 used under the same conditions. Step-wise recovery of shoot tips on ammonium-free medium followed by GA₃-containing medium and medium without growth regulators were critical for the normal regeneration of both VS-treated and cryopreserved shoot tips.

CONCLUSIONS

Cryopreservation of in vitro shoot tips using droplet-vitrification was developed as a complementary conservation approach for A. altaicus. Adjustment of the composition of regrowth media depending on recovery stage was important for the regeneration of healthy plants from cryopreserved shoot tips.

A magnetically driven piston pump for ultra-clean applications

A magnetically driven piston pump for xenon gas recirculation is presented. The pump is designed to satisfy extreme purity and containment requirements, as is appropriate for the recirculation of isotopically enriched xenon through the purification system and large liquid xenon time projection chamber of EXO-200. The pump, using sprung polymer gaskets, is capable of pumping more than 16 standard liters per minute of xenon gas with 750 Torr differential pressure.

Development of co-selected single nucleotide polymorphisms in the viral promoter precedes the onset of human immunodeficiency virus type 1-associated neurocognitive impairment

The long terminal repeat (LTR) regulates gene expression of HIV-1 by interacting with multiple host and viral factors. Cross-sectional studies in the pre-HAART era demonstrated that single nucleotide polymorphisms (SNPs) in peripheral blood-derived LTRs (a C-to-T change at position 3 of C/EBP site I (3T) and at position 5 of Sp site III (5T)) increased in frequency as disease severity increased. Additionally, the 3T variant correlated with HIV-1-associated dementia. LTR sequences derived by longitudinal sampling of peripheral blood from a single patient in the DrexelMed HIV/AIDS Genetic Analysis Cohort resulted in the detection of the 3T and 5T co-selected SNPs before the onset of neurologic impairment, demonstrating that these SNPs may be useful in predicting HIV-associated neurological complications. The relative fitness of the LTRs containing the 3T and/or 5T co-selected SNPs as they evolve in their native patient-derived LTR backbone structure demonstrated a spectrum of basal and Tat-mediated transcriptional activities using the IIIB-derived Tat and colinear Tat derived from the same molecular clone containing the 3T/5T LTR SNP. In silico predictions utilizing colinear envelope sequence suggested that the patient's virus evolved from an X4 to an R5 swarm prior to the development of neurological complications and more advanced HIV disease. These results suggest that the HIV-1 genomic swarm may evolve during the course of disease in response to selective pressures that lead to changes in prevalence of specific polymorphisms in the LTR, env, and/or tat that could predict the onset of neurological disease and result in alterations in viral function.

Disrupted theory of mind network processing in response to idea of reference evocation in schizophrenia

OBJECTIVE

This study examined the neural pathophysiology of the theory of mind network by eliciting self-referential processing during an idea of reference evocating situation in patients with schizophrenia.

METHOD

Functional MRI was conducted on 14 schizophrenic in-patients with the idea of reference and 15 healthy participants while viewing video vignettes of referential conversations, non-referential conversations or no conversations between two people, which were filmed at varying distances of 1, 5 or 10 m.

RESULTS

The patient group did not show normal patterns of superior temporal sulcus activation to conversational context, and reciprocal deactivation and activation of the ventromedial and dorsomedial prefrontal cortex to referential conversational context. Instead, the patient group showed overall greater ventromedial prefrontal activities across different conversational contexts and inverse correlation between superior temporal sulcus activity and delusional severity. Differential activations of the temporal pole and its posterior extension to varying distances were observed in the control group but not in the patient group.

CONCLUSION

The present study demonstrates that theory of mind-related responses of the medial prefrontal-superior temporal network are attenuated during the self-referential processing in patients with schizophrenia and that these abnormalities may be related to the formation of their referential or persecutory delusion.

Assessment of post-stroke extrapersonal neglect using a three-dimensional immersive virtual street crossing program

OBJECTIVE

To investigate the potential of our newly developed three-dimensional immersive virtual reality (VR) program modeled on a real street crossing as an assessment tool for extrapersonal neglect in stroke patients.

METHODS

Thirty-two patients with right-hemispheric stroke (neglect group, 16; non-neglect group, 16) were enrolled. The deviation angle, reaction time, left-to-right reaction time ratio, visual and auditory cue rates, and failure rate were evaluated during missions to keep a virtual avatar safe from a traffic accident in the VR program. The line bisection test and letter cancellation test were also evaluated.

RESULTS

The deviation angle, left-to-right reaction time ratio, left visual and auditory cue rates and left failure rate in the VR program showed significant differences between the two groups (P < 0.05). Depending on the direction of approach of the virtual car, the left parameters were significantly higher than the right parameters in the neglect group (P < 0.05). In the neglect group, the line bisection test correlated significantly with the deviation angle (P < 0.05). None of the other virtual reality parameters significantly correlated with the paper and pencil tests.

CONCLUSION

Post-stroke neglect in the extrapersonal space can be easily and safely detected and measured using our three-dimensional immersive virtual street crossing program.

Syringomatous adenoma of the nipple

Infiltrating syringomatous adenoma (SA) of the nipple is a rare but distinct benign clinical entity affecting the breast. It needs to be included in the differential diagnosis of patients who present with a lump in the nipple/areola complex. It is similar histologically to a syringoma, a benign tumour originating in the ducts of the dermal sweat glands, and importantly needs to be distinguished from a tubular carcinoma. SA of the nipple is locally infiltrating but is not known to metastasise. It often presents as a subareolar lesion with clinical, mammographic and ultrasound findings suspicious for malignancy. Whilst it may be possible to suspect the diagnosis on fine needle cytology, core biopsy or excisional biopsy is usually required to establish the diagnosis. There is a tendency to recurrence if excision is incomplete. The following is a case report, literature review and discussion of the surgical management options available in this unusual condition.

Stapled versus sutured gastrointestinal anastomoses in the trauma patient: a multicenter trial

BACKGROUND

Construction of gastrointestinal anastomoses utilizing stapling devices has become a familiar procedure. In elective surgery, studies have shown no significant differences in complications between stapled and sutured anastomoses. Controversy has recently arisen regarding the accurate incidence of complications associated with anastomoses in the trauma patient. The objective of this multi-institutional study was to determine whether the incidence of postoperative complications differs between stapled and sutured anastomoses following the emergent repair of traumatic bowel injuries.

METHODS

Using a retrospective cohort design, all trauma registry records from five Level I trauma centers over a period of 4 years were reviewed.

RESULTS

A total of 199 patients with 289 anastomoses were identified. A surgical stapling device was used to create 175 separate anastomoses, while a hand-sutured method was employed in 114 anastomoses. A complication was defined as an anastomotic leak verified at reoperation, an intra-abdominal abscess, or an enterocutaneous fistula. The mean abdominal Abbreviated Injury Scale score and Injury Severity Score were similar in the two cohort groups. Stapling and suturing techniques were evenly distributed in both small and large bowel repairs. Seven of the total 175 stapled anastomoses and none of the 114 hand-sewn anastomoses resulted in a clinically significant leak requiring reoperation (RR = undefined, 95% CI 1.08-infinity, p = 0.04). Each anastomotic leak occurred in a separate individual. Nineteen stapled anastomoses and four sutured anastomoses were associated with an intra-abdominal abscess (RR = 2.7, 95% CI 0.96-7.57, p = 0.04). Enterocutaneous fistula formation was not statistically associated with either type of anastomoses (stapled cohort = 3 of 175 and sutured cohort = 2 of 114). Overall, 22 (13%) stapled anastomoses and 6 (5%) sutured anastomoses were associated with an intra-abdominal complication (RR = 2.08, 95% CI 0.89-4.86, p = 0.076).

CONCLUSION

Anastomotic leaks and intra-abdominal abscesses appear to be more likely with stapled bowel repairs compared with sutured anastomoses in the injured patient. Caution should be exercised in deciding to staple a bowel anastomosis in the trauma patient.

Development of virtual environment for treating acrophobia

Virtual Reality (VR) is a new technology that makes humans communicate with computer. It allows the user to see, hear, feel and interact in a three-dimensional virtual world created graphically. Virtual Reality Therapy (VRT), based on this sophisticated technology, has been recently used in the treatment of subjects diagnosed with acrophobia, a disorder that is characterized by marked anxiety upon exposure to heights, avoidance of heights, and a resulting interference in functioning. Conventional virtual reality system for the treatment of acrophobia has a limitation in scope that it is based on over-costly devices or somewhat unrealistic graphic scene. The goal of this study was to develop a inexpensive and more realistic virtual environment for the exposure therapy of acrophobia. We constructed two types virtual environment. One is constituted a bungee-jump tower in the middle of a city. It includes the open lift surrounded by props beside tower that allowed the patient to feel sense of heights. Another is composed of diving boards which have various heights. It provides a view of a lower diving board and people swimming in the pool to serve the patient stimuli upon exposure to heights.

Alteration in Kupffer cell function after mild hemorrhagic shock

Functional changes in Kupffer cells occur after profound hemorrhagic shock. This study was performed to demonstrate if Kupffer cell changes also occur after mild hemorrhagic shock. Sprague-Dawley rats were bled to a systolic blood pressure of 60 to 70 mmHg and resuscitated with Lactated Ringers solution (twice the shed blood volume) after 30 min. Resuscitation produced immediate recovery of blood pressure and allowed long-term recovery of the animals. Sham animals received anesthesia and monitoring only. Thirty minutes after resuscitation, Kupffer cells were isolated by centrifugal elutriation and cultured for 48 h. In Kupffer cells isolated from shocked animals, phorbol ester-stimulated superoxide production increased 7-fold and lipopolysaccharide- (LPS) stimulated prostaglandin E2 (PGE2) production increased 4-fold. Tumor necrosis factor-alpha (TNFalpha) production, on the other hand, was decreased by 50%. A non-significant trend toward increased phagocytosis was also observed, whereas LPS-stimulated nitric oxide production was unchanged. In conclusion, mild hemorrhagic shock produced increases in superoxide and PGE2 production, and decreases in TNFalpha production by Kupffer cells, changes that may be appropriate to defend against the infectious challenges that often follows trauma and hemorrhage.

Performance characteristics of the COBAS AmpliScreen HIV-1 test, version 1.5, an assay designed for screening plasma mini-pools

BACKGROUND

The COBAS AmpliScreen HIV-1 test, version 1.5 (v1.5) (Roche Molecular Systems), is designed for screening pools composed of samples from 24 individual units of blood or plasma. A specimen-processing procedure (Multiprep) simultaneously concentrates and extracts HIV-1, HCV, and HBV particles from plasma and incorporates an HIV-1 internal control (IC) RNA. Processed samples are amplified by RT-PCR using HIV-1-specific primers and detected by hybridization of the amplified products to HIV-1- and IC-specific oligonucleotide probes.

STUDY DESIGN AND METHODS

Plasma samples containing known quantities of HIV-1 were used to evaluate analytical sensitivity and precision and to validate a pool testing algorithm. Analytical specificity was evaluated by adding various viruses and bacteria to HIV-1-negative plasma. Seroconversion panels were tested to estimate the window-period reduction achieved by RNA testing.

RESULTS

The analytical sensitivity of the test (concentration that yields > or = 95% positive results in a set of replicate tests) was 25 copies of HIV-1 RNA per mL of pooled plasma. Representative strains from all HIV-1 group M subtypes were reproducibly detected (> 95% positive results) at concentrations of 20 to 200 viral particles per mL. The test did not cross-react with a set of 31 viral and 5 bacterial isolates, and it yielded negative results on a panel of 500 blood samples from HIV-1-seronegative donors. Plasma samples containing abnormally high levels of Hb, albumin, triglycerides, or bilirubin did not interfere with the test. HIV-1 RNA was detected 2 to 14 days before HIV-1 antibody and 0 to 28 days before p24 antigen. The test specifically detected pools containing a single positive unit with 2400 HIV-1 RNA copies per mL and correctly identified the positive unit.

CONCLUSION

The COBAS AmpliScreen HIV-1 test, v1.5, has sufficient sensitivity to detect a single infected unit containing 600 copies of HIV-1 per mL in a pool with 23 uninfected units and should reduce the window period between infection and seroconversion by at least 2 to 14 days.

Nifedipine controlled delivery by sandwiched osmotic tablet system

The sandwiched osmotic tablet system (SOTS), which is composed of a sandwiched osmotic tablet core surrounded by a cellulose acetate membrane with two orifices on both side surfaces, has been successfully prepared with the purpose of delivering nifedipine. The sandwiched osmotic tablet core consists of a middle push layer and two attached drug layers. Influences of tablet formulation variables, orifice size and membrane variables on nifedipine release of SOTS have been studied. It was found that potassium chloride amount of push layer and polyethylene oxide amount of drug layer had markedly positive effects on nifedipine release. A push layer/drug layer co-controlled osmotic delivery mechanism and the optimal core formulation have been proposed. The appropriate orifice size was observed in the range of 0.50-1.41 mm. It was also found that the drug release rate of SOTS could be increased by incorporating hydrophilic plasticizer in the membrane, whereas it decreased with hydrophobic plasticizer. It has been observed that the SOTS gives fairly comparable in vitro release features as that of commercialized push-pull osmotic tablet system, such as an approximately constant rate up to 24 h and independence of release media and agitation rate. Exempting side identification before drilling, it is easier to prepare the SOTS than the push-pull osmotic tablet system.

Simultaneous extraction of hepatitis C virus (HCV), hepatitis B virus, and HIV-1 from plasma and detection of HCV RNA by a reverse transcriptase-polymerase chain reaction assay designed for screening pooled units of donated blood

BACKGROUND

Testing for viral nucleic acids should reduce the residual risk of transmitting viral infections by transfusion of blood components. The AmpliScreen Hepatitis C (HCV) Test, Version 2.0, was designed for screening pools composed of samples from individual units of blood or plasma.

STUDY DESIGN AND METHODS

An ultracentrifugation step during sample processing simultaneously extracts and concentrates HCV, HIV type 1, and hepatitis B virus particles from plasma. An HCV internal control RNA serves as an extraction and amplification control for each processed sample. Processed samples are amplified by reverse transcriptase polymerase chain reaction and detected by hybridization of the amplified products to HCV- and internal-control-specific oligonucleotide probes. Plasma samples containing known quantities of HCV were used to evaluate analytical sensitivity and precision.

RESULTS

The analytical sensitivity of the test was 25 IU of HCV per mL of pooled plasma; all HCV genotypes were detected with similar efficiency. The test did not react with other blood-borne viruses. The within-run and total coefficients of variation were 1.3-13.0 percent and 1.7-22.0 percent, respectively, with low copy samples producing the more variable results. The test performed well using plasma collected in either EDTA, ACD, or PPT Vacutainer tubes. Plasma samples containing elevated levels of hemoglobin, albumin, triglycerides, or bilirubin did not interfere with the test. The test detected HCV RNA 23 to 32 days prior to seroconversion for four of the five seroconversion panels tested.

CONCLUSION

The AmpliScreen HCV Test, Version 2.0 provides a reproducible and specific method for screening pooled blood units for HCV. Theoretically, this test has sufficient sensitivity to detect a single infected unit containing 2.4 x 10(3) IU of HCV per mL in a pool with 95 uninfected units and should reduce the window period by at least 20 to 30 days.

Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli

The fmu gene product has been proposed to be an RNA methyltransferase [Koonin, E. V. (1994) Nucleic Acids Res. 22, 2476-2478]. Fmu has been cloned and expressed, and the encoded 47 kDa protein has been purified and characterized. The enzyme catalyzed specific methylation of C967 of unmodified 16S rRNA transcripts. A 16mer stem-loop structure containing C967 (nt 960-975) was also a good substrate for the enzyme in vitro. Methylation of C967 was confirmed by several methods including analysis of RNase T1 digests and nearest-neighbor analysis. Fmu did not catalyze methylation of transcripts of 23S rRNA. E. coli cells that contained kanr-disrupted fmu produced 16S rRNA that could be specifically methylated by Fmu in vitro at C967 but not C1407. Further, fmu disruption did not significantly alter the growth rate of E. coli in rich or minimal media. We propose renaming this ORF "rrmB" and the enzyme "RrmB" for rRNA methyltransferase.

Identification of two Escherichia coli pseudouridine synthases that show multisite specificity for 23S RNA

Several putative Escherichia coli pseudouridine (Psi) synthases have been identified by iterative searching of genomic databases for ORFs homologous to known Psi synthases [Gustafsson et al. (1996) Nucleic Acids Res. 24, 3756-3762]. Of these, yceC and yfiI were proposed to encode Psi synthases which modify 23S rRNA. In the present work, yceC and yfiI were cloned and overexpressed in E. coli, and the encoded enzymes, YceC and YfiI, were purified to homogeneity. Both proteins converted Urd residues of rRNA to Psi, thus confirming their identities as Psi synthases. However, in in vitro experiments both enzymes extensively modified Urd residues of both 23S rRNA and 16S rRNA. Gene-disruption of yceCresulted in the absence of Psi modification at positions U955, 2504, and 2580 of 23S RNA, thus identifying these sites as in vivo targets for YceC. Likewise, yfiI disruption resulted in the absence of Psi modification at positions U1911, 1917, and possibly 1915 of 23S RNA. Disruption of yceC did not affect the growth under the conditions tested, whereas yfiI-disrupted cells showed a dramatic decrease in growth rate. Since YceC and YfiI hypermodify RNA in vitro, factors in addition to ribonucleotide sequence must contribute to the in vivo specificity of these enzymes.

Ultrasensitive reverse transcription-PCR assay for quantitation of human immunodeficiency virus type 1 RNA in plasma

With the recent introduction of combination therapy, human immunodeficiency virus type 1 (HIV-1) RNA levels in plasma have been dramatically reduced, frequently to below the limit of quantitation (400 copies/ml of plasma) of the AMPLICOR HIV-1 MONITOR Test (Roche Diagnostic Systems). To achieve enhanced sensitivity of the AMPLICOR HIV-1 MONITOR Test, a modified specimen preparation procedure that allows input of RNA from 10-fold more plasma per amplification reaction was developed. This "ultrasensitive" method allows the accurate quantitation of plasma HIV-1 RNA levels as low as 50 copies/ml. A precision study yielded average within-run and between-run coefficients of variation (CV) of 24.8 and 9.6%, respectively. A multicenter reproducibility study demonstrated that the laboratory-to-laboratory reproducibility of this assay is good, with an average CV of 32%. The linear range of this test is between 50 and 50,000 copies/ml of plasma. RNA concentrations measured by the ultrasensitive and standard HIV-1 MONITOR tests exhibited good agreement within the shared linear range of the two methods. The two measurements were within a factor of 2 for 91% of the specimens tested, with the concentration measured by the ultrasensitive method being only slightly lower (median, 22% lower). Preliminary studies suggest that this assay will prove to be useful for predicting the stability of viral suppression in patients whose RNA levels drop below 400 copies/ml in response to highly active antiretroviral therapy.

Nitric oxide inhibits peroxide-mediated endothelial toxicity

BACKGROUND

Oxidant molecules and nitric oxide (NO) have each been implicated as mediators of endothelial cell damage, but the biologic effect of these molecules acting in concert is incompletely understood.

MATERIALS AND METHODS

We studied the effects of an NO donor, S-nitroso-acetyl-D,L-penicillamine (SNAP), in combination with the peroxidants tert-butyl hydroperoxide (TBH) and hydrogen peroxide (H2O2) on rabbit aortic endothelial cells in culture. Cell viability was assessed using Alamar blue, a nontoxic dye indicator of cell metabolism. Lipid peroxidation was assessed using a chemiluminescent single-photon counting technique.

RESULTS

After 90 min exposure to test reagents, there was concentration-dependent cytotoxicity for both TBH and H2O2. Peroxidant-induced cytotoxicity was significantly ameliorated by SNAP (10(-4)-10(-3)M). N-Acetylpenicillamine and NO-depleted SNAP failed to demonstrate a cytoprotective effect against peroxidant cellular injury, thus implicating NO as the agent responsible for the protective effect. SNAP reduced lipid peroxidation caused by 10(-3) M TBH in a dose-dependent manner. Preincubation of cells with SNAP before exposure to peroxidants alone had no effect on toxicity.

CONCLUSIONS

NO is cytoprotective to the endothelium in the presence of peroxidants through a reduction of lipid peroxidation.

Expression of a functional non-ribosomal peptide synthetase module in Escherichia coli by coexpression with a phosphopantetheinyl transferase

BACKGROUND

Non-ribosomal peptide synthetases (NRPSs) found in bacteria and fungi are multifunctional enzymes that catalyze the synthesis of a variety of biologically important peptides. These enzymes are composed of modular units, each responsible for the activation of an amino acid to an aminoacyl adenylate and for the subsequent formation of an aminoacyl thioester with the sulfhydryl group of a 4'-phosphopantetheine moiety. Attempts to express these modules in Escherichia coli have resulted in recombinant proteins deficient in 4'-phosphopantetheine. The recent identification of a family of phosphopantetheinyl transferases (P-pant transferases) associated with NRPS have led us to investigate whether coexpression of NRPS modules with P-pant transferases in E. coli would lead to the incorporation of 4'-phosphopantetheine.

RESULTS

A truncated module of gramicidin S synthetase, PheAT(His6), was expressed as a His6 fusion protein in E. coli with and without Gsp, the P-pant transferase associated with gramicidin S synthetase. Although PheAT(His6) expressed alone in E. coli catalyzed Phe-AMP formation from Phe and ATP, <1% was converted to the Phe thioester. In contrast, >80% of the PheAT(His6) that was coexpressed with Gsp could form the Phe thioester in the presence of Phe and ATP.

CONCLUSIONS

Our finding indicates the presence of an almost equimolar amount of 4'-phosphopantetheine covalently bound to the NRPS module PheAT(His6), and that the functional expression of NRPS modules in E. coli is possible, provided that they are coexpressed with an appropriate P-pant transferase.

Alternate protein frameworks for molecular recognition

In an effort to determine whether proteins with structures other than the immunoglobulin fold can be used to mimic the ligand binding properties of antibodies, we generated a library from the four-helix bundle protein cytochrome b562 in which the two loops were randomized. Panning of this library against the bovine serum albumin (BSA) conjugate of N-methyl-p-nitrobenzylamine derivative 1 by phage display methods yielded cytochromes in which residues Trp-20, Arg-21, and Ser-22 in loop A and Arg-83 and Trp-84 in loop B were conserved. The individual mutants, which fold into native-like structure, bind selectively to the BSA-1 conjugate with micromolar dissociation constants (Kd), in comparison to a monoclonal antibody that binds selectively to 1 with a Kd of 290 nM. These and other antibody-like receptors may prove useful as therapeutic agents or as reagents for both intra- and extracellular studies.