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B A Shapiro

Publications and source records attributed to B A Shapiro.

At least 55 records · Page 3Linked to original sources
PubMed1993

Identification of a binding site for the human immunodeficiency virus type 1 nucleocapsid protein.

The nucleocapsid (NC) protein NCp7 of human immunodeficiency virus type 1 (HIV-1) is important for encapsidation of the virus genome, RNA dimerization, and primer tRNA annealing in vitro. Here we present evidence from gel mobility-shift experiments indicating that NCp7 binds specifically to an RNA sequence. Two complexes were identified in native gels. The more slowly migrating complex contained two RNA molecules and one peptide, while the more rapidly migrating one is composed of one RNA and one peptide. Further, mutational analysis of the RNA shows that the predicted stem and loop structure of stem-loop 1 plays a critical role. Our results show that NCp7 binds to a unique RNA structure within the psi region; in addition, this structure is necessary for RNA dimerization. We propose that NCp7 binds to the RNA via a direct interaction of one zinc-binding motif to stem-loop 1 followed by binding of the other zinc-binding motif to stem-loop 1, stem-loop 2, or the linker region of the second RNA molecule, forming a bridge between the two RNAs.

Base Sequence↗
PubMed1993

Clinical performance of a blood gas monitor: a prospective, multicenter trial.

OBJECTIVE: To prospectively assess the clinical performance of a fluorescent optode-based blood gas monitoring system that is designed to perform arterial pH, PCO2, and PO2 measurements as frequently as clinically required without violating the integrity of the arterial catheter tubing system or permanently removing blood from the patient. DESIGN: A prospective, multicenter study to compare modern blood gas analyzer measurements with the coinciding measurements of the blood gas monitoring system. SETTING: Four intensive care units (ICUs) in academic centers with varying patient populations, blood gas measurement routines, and blood gas laboratory facilities. PATIENTS: Adult ICU patients (n = 117), with appropriately functioning radial arterial catheters in place, who were assessed as likely to require multiple arterial blood gas measurements for > or = 2 days. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: A total of 117 patients had 1,341 concurrent blood gas analyzer and monitor measurements of arterial pH, PCO2, and PO2 over a 1- to 4-day period. The range of values were 7.14 to 7.64 for arterial pH, 19 to 98 torr (2.5 to 13.0 kPa) for PaCO2, and 38 to 413 torr (5.1 to 54.9 kPa) for PaO2. Linear regression analysis of the optode-based monitor compared with the electrode-based blood gas analyzer demonstrated r2 values of .85 for pH, .92 for PCO2, and .94 for PO2. Comparative statistical analyses for bias (mean difference between analyzer and monitor) and precision (standard deviation of the mean difference [+/- SD] between analyzer and monitor) were respectively:-0.004 and +/- 0.027 for pH; -0.8 torr (-0.11 kPa) and +/- 2.4 torr (0.32 kPa) for PCO2; -2.2 torr (-0.31 kPa) and +/- 8.7 torr (1.2 kPa) for PO2. CONCLUSIONS: Clinical performance of this fluorescent, optode-based blood gas monitoring system demonstrates stability, consistency, and accuracy comparable to modern blood gas analyzers. This system withstood the normal abuse and rigors of clinical conditions common to the ICU while reliably performing in critically ill patients for up to 80 hrs. Use of the device did not significantly alter the function or longevity normally expected from a 20-gauge radial artery catheter. We submit that this blood gas monitoring system can replace the use of blood gas analyzers for ICU patients with indwelling arterial catheters.

Adolescent↗
PubMed1992

Extensive sequence-specific information throughout the CAR/RRE, the target sequence of the human immunodeficiency virus type 1 Rev protein.

The significance and location of sequence-specific information in the CAR/RRE, the target sequence for the Rev protein of the human immunodeficiency virus type 1 (HIV-1), have been controversial. We present here a comprehensive experimental and computational approach combining mutational analysis, phylogenetic comparison, and thermodynamic structure calculations with a systematic strategy for distinguishing sequence-specific information from secondary structural information. A target sequence analog was designed to have a secondary structure identical to that of the wild type but a sequence that differs from that of the wild type at every position. This analog was inactive. By exchanging fragments between the wild-type sequence and the inactive analog, we were able to detect an unexpectedly extensive distribution of sequence specificity throughout the CAR/RRE. The analysis enabled us to identify a critically important sequence-specific region, region IIb in the Rev-binding domain, strongly supports a proposed base-pairing interaction in this location, and places forceful constraints on mechanisms of Rev action. The generalized approach presented can be applied to other systems.

Base Sequence↗
PubMed1992

Concurrent bacterial lung infection in patients with AIDS, PCP, and respiratory failure.

STUDY OBJECTIVES: To determine and compare the incidence of concurrent bacterial lung infection in intubated and nonintubated patients with the acquired immunodeficiency syndrome (AIDS) and Pneumocystis carinii pneumonia (PCP) requiring medical intensive care unit (MICU) admission for support of their respiratory function. DESIGN: Retrospective review of medical records. SETTING: A large university hospital and AIDS treatment center. PATIENTS: All AIDS/PCP patients admitted to the MICU for support of oxygenation and/or ventilation between 1985 and 1989. Survival was defined as discharge from the hospital; nonsurvival was defined as death any time during the hospitalization. Patients with acute spinal cord injury (SCI) were used as controls to determine the incidence of nosocomial pneumonia in ICU patients of similar age without AIDS. MEASUREMENTS AND RESULTS: Twenty-nine AIDS/PCP patients met study criteria; eight (28 percent) were survivors and 21 (72 percent) were nonsurvivors. There was no significant difference in duration of intubation or duration of ICU stay between survivors and nonsurvivors with or without intubation. The incidence of bacterial concurrent lung infection (CLI) in AIDS/PCP patients overall was 7 percent and in intubated AIDS/PCP patients it was 10 percent. There was no statistically significant difference in the incidence of bacterial CLI between the survivors and nonsurvivors or between intubated and nonintubated patients with AIDS/PCP. The incidence of nosocomial pneumonia in SCI overall was 17 percent and in intubated SCI patients it was 30 percent. CONCLUSIONS: The incidence of bacterial lung infections in our retrospective study of AIDS patients with PCP is remarkably less than in the general ICU population with respiratory failure and in our control patients with SCI, although the differences did not attain statistical significance. This finding may be related to antimicrobial therapy directed against P carinii. Endotracheal intubation in patients with AIDS and PCP, who were undergoing appropriate antimicrobial therapy, did not result in a significantly higher incidence of bacterial lung infections than in those who were not intubated. There was no significant difference in the incidence of bacterial lung infections between those AIDS/PCP patients who survived episodes of severe respiratory failure and those who did not. Endotracheal intubation should not be delayed or withheld from this patient population due to concerns of pulmonary bacterial superinfection.

Acquired Immunodeficiency Syndrome↗
PubMed1991

Functional importance of sequence in the stem-loop of a transcription terminator.

Intrinsic transcription terminators of prokaryotes are distinguished by a common RNA motif: a stem-loop structure high in guanine and cytosine content, followed by multiple uridine residues. Models explaining intrinsic terminators postulate that the stem-loop sequence is necessary only to form structure. In the tR2 terminator of coliphage lambda, single-nucleotide changes reducing potential RNA stem stability eliminated tR2 activity, and a compensatory change that restored the stem structure restored terminator activity. However, multiple changes in the stem sequence that should have either maintained or increased stability reduced terminator activity. These results suggest that the ability of the stem-loop structure to signal transcription termination depends on sequence specificity and secondary structure.

Bacteriophage lambda↗
PubMed1991

RNA pseudoknots downstream of the frameshift sites of retroviruses.

RNA pseudoknot structural motifs could have implications for a wide range of biological processes of RNAs. In this study, the potential RNA pseudoknots just downstream from the known and suspected retroviral frame-shift sites were predicted in the Rous sarcoma virus, primate immunodeficiency viruses (HIV-1, HIV-2, and SIV), equine infectious anemia virus, visna virus, bovine leukemia virus, human T-cell leukemia virus (types I and II), mouse mammary tumor virus, Mason-Pfizer monkey virus, and simian SRV-1 type-D retrovirus. Also, the putative RNA pseudoknots were detected in the gag-pol overlaps of two retrotransposons of Drosophila, 17.6 and gypsy, and the mouse intracisternal A particle. For each sequence, the thermodynamic stability and statistical significance of the secondary structure involved in the predicted tertiary structure were assessed and compared. Our results show that the stem-loop structures in the pseudoknots are both thermodynamically highly stable and statistically significant relative to other such configurations that potentially occur in the gag-pol or gag-pro and pro-pol junction domains of these viruses (300 nucleotides upstream and downstream from the possible frameshift sites are included). Moreover, the structural features of the predicted pseudoknots following the frameshift site of pro-pol overlaps of the HTLV-1 and HTLV-2 retroviruses are structurally well conserved. The occurrence of eight compensatory base changes in the tertiary interaction of the two related sequences allow the conservation of their tertiary structures in spite of the sequence divergence. The results support the possible control mechanism for frameshifting proposed by Brierley et al. and Jacks et al.

Base Sequence↗
PubMed1991

Intensive care unit patients with acquired immunodeficiency syndrome and Pneumocystis carinii pneumonia: suggested predictors of hospital outcome.

OBJECTIVE: To define our ICU experience with AIDS patients, Pneumocystis carinii pneumonia, and respiratory failure, and to delineate factors predictive of hospital survival. DESIGN: A retrospective study in which logistic regression analysis was applied to data obtained during the first 144 hrs of ICU admission. SETTING: A university hospital medical ICU associated with a national AIDS treatment center. PATIENTS: Twenty-seven male patients with AIDS, P. carinii pneumonia, and respiratory failure who desired full supportive and resuscitative care. MEASUREMENTS AND MAIN RESULTS: Of 27 patients who met study criteria, 19 (70%) were nonsurvivors and eight (30%) were survivors. The relative risk of death was 2.2 times greater in patients who exhibited the combination of pH less than 7.35 and a base deficit greater than 4 mEq/L, at any time in their ICU course, than in patients who did not (95% confidence interval = 1.01, 4.81). Furthermore, the relative risk of death was 3.7 times greater in patients who required positive end-expiratory pressure greater than 10 cm H2O after 96 hrs of ICU care than in those patients who did not (95% confidence interval = 1.09, 12.33). Indices of oxygen transfer, severity of chest radiograph abnormalities, concurrent lung infections, and most laboratory studies on hospital admission were not different between the two groups nor predictive of hospital survival. CONCLUSIONS: When dealing with AIDS/P. carinii pneumonia/ICU patients, it is not possible to distinguish who will survive to hospital discharge based on information routinely available before ICU admission. Those patients with the greatest chance of survival demonstrate a significant decrease in the required level of respiratory support within the first 4 days of ICU care. The presence of a metabolic acidemia (pH less than 7.35 and base deficit greater than 4 mEq/L), at any time during the ICU course, is a poor prognostic sign. We suggest that such objective variables should be included in the development of any new outcome predictor model for this group of ICU patients.

Acquired Immunodeficiency Syndrome↗
PubMed1991

Airway pressure release ventilation in severe acute respiratory failure.

Airway pressure release ventilation (APRV), a new ventilatory support technique, was compared with conventional intermittent positive-pressure ventilation plus PEEP (CPPV) in 18 patients with severe acute respiratory failure. Patients were initially stabilized on CPPV and then switched to APRV. The APRV provided effective ventilatory support in 17 of 18 patients; APRV achieved similar levels of alveolar ventilation as CPPV (for APRV, mean PaCO2 = 45.0 +/- 6.2 mm Hg; vs for CPPV, mean PaCO2 = 43.3 +/- 5.7 mm Hg), with significantly lower mean maximum airway pressures (38.9 +/- 10.1 cm H2O vs 64.6 +/- 15.4 cm H2O; p = 0.0001) and mean VT (0.79 +/- 0.11 L vs 1.05 +/- 0.15 L; p = 0.0002). No significant differences in mean airway pressure, end-expiratory pressure, FIO2, ventilator rate, arterial blood gas levels, and hemodynamic function were noted between APRV and CPPV.

Acute Disease↗
PubMed1990

Comparing multiple RNA secondary structures using tree comparisons.

In a previous paper, an algorithm was presented for analyzing multiple RNA secondary structures utilizing a multiple string alignment algorithm. In this paper we present another approach to the problem of comparing many secondary structures by utilizing a very efficient tree-matching algorithm that will compare two trees in O([T1] X [T2] X L1 X L2) in the worst case and very close to O([T1] X [T2]) for average trees representing secondary structures. The result of the pairwise comparison algorithm is then used with a cluster algorithm to produce a multiple structure clustering which can be displayed in a taxonomy tree to show related structures.

Algorithms↗
PubMed1989

Detection of common motifs in RNA secondary structures.

We describe a novel computerized system for comparison of RNA secondary structures and demonstrate its use for experimental studies. The system is able to screen a very large number of structures, to cluster similar structures and to detect specific structural motifs. In particular, the system is useful for detecting mutations with specific structural effects among all possible point mutations, and for predicting compensatory mutations that will restore the wild type structure. The algorithms are independent of the folding rules that are used to generate the secondary structures.

Algorithms↗