Yeast TOR signaling: a mechanism for metabolic regulation

Understanding how cell growth is regulated in response to environmental signals remains a challenging biological problem. Recent studies indicate the TOR (target of rapamycin) kinase acts within an intracellular regulatory network used by eukaryotic cells to regulate their growth according to nutrient availability. This network affects all aspects of gene expression, including transcription, translation, and protein stability, making TOR an excellent candidate as a global regulator of cellular activity. Here we review our recent studies of two specific transcriptional outputs controlled by TOR in the budding yeast, S. cerevisiae: (1) positive regulation of genes involved in ribosome biogenesis, and (2) negative regulation of genes required for de novo biosynthesis of glutamate and glutamine. These studies have raised the important issue as to how diverse nutritional cues can pass through a common signaling pathway and yet ultimately generate distinct transcriptional responses.

Mechanism of metabolic control. Target of rapamycin signaling links nitrogen quality to the activity of the Rtg1 and Rtg3 transcription factors

De novo biosynthesis of amino acids uses intermediates provided by the TCA cycle that must be replenished by anaplerotic reactions to maintain the respiratory competency of the cell. Genome-wide expression analyses in Saccharomyces cerevisiae reveal that many of the genes involved in these reactions are repressed in the presence of the preferred nitrogen sources glutamine or glutamate. Expression of these genes in media containing urea or ammonia as a sole nitrogen source requires the heterodimeric bZip transcription factors Rtg1 and Rtg3 and correlates with a redistribution of the Rtg1p/Rtg3 complex from a predominantly cytoplasmic to a predominantly nuclear location. Nuclear import of the complex requires the cytoplasmic protein Rtg2, a previously identified upstream regulator of Rtg1 and Rtg3, whereas export requires the importin-beta-family member Msn5. Remarkably, nuclear accumulation of Rtg1/Rtg3, as well as expression of their target genes, is induced by addition of rapamycin, a specific inhibitor of the target of rapamycin (TOR) kinases. We demonstrate further that Rtg3 is a phosphoprotein and that its phosphorylation state changes after rapamycin treatment. Taken together, these results demonstrate that target of rapamycin signaling regulates specific anaplerotic reactions by coupling nitrogen quality to the activity and subcellular localization of distinct transcription factors.

Effectiveness of palivizumab: evaluation of outcomes from the 1998 to 1999 respiratory syncytial virus season. The Palivizumab Outcomes Study Group

BACKGROUND

Respiratory syncytial virus (RSV) remains a significant cause of morbidity, especially in premature infants and immunocompromised children, resulting in approximately 100 000 hospitalizations annually. A study was performed to evaluate the outcomes of those given palivizumab (Synagis; MedImmune, Inc., Gaithersburg, MD) during the 1998 to 1999 RSV season, its first season in general use.

METHODS

A retrospective chart review of 1839 patients from 9 United States sites was conducted, representing all patients given palivizumab at each site. Those evaluated were to have a gestational age of < or =35 weeks, were to be <2 years old at their first injection and were to have received at least one dose of palivizumab (humanized monoclonal antibody against RSV) between September, 1998, and May, 1999. Gestational age, comorbidities, frequency of injections, hospitalizations and length of hospital stays were assessed.

RESULTS

The antigen- or culture-positive RSV hospitalization rates for those given prophylaxis were 2.3% (42 of 1839) overall, 16/399 (4.0%) with chronic lung disease of infancy and 26 of 1227 (2.1%) born prematurely without chronic lung disease of infancy. Twenty-six patients had a gestational age of >35 weeks and were included in the analysis.

CONCLUSIONS

Only 2.3% of children receiving palivizumab prophylaxis were hospitalized with RSV lower respiratory infection. This compares favorably with the rates observed in the pivotal trial (IMpact-RSV trial in 1996 to 1997), in which prophylaxis reduced hospitalization from 10.6% in the placebo group to 4.8% in those children receiving prophylaxis.

Determinants of power-frequency magnetic fields in residences located away from overhead power lines

The Wertheimer-Leeper wire code, originally developed as a surrogate for magnetic-field exposure, has been associated with childhood leukemia in several epidemiologic investigations. However, these and other studies indicate that most between-residence variability in measured magnetic fields remains unexplained by wire codes. To better understand this remaining variability, engineering and demographic data were examined for 333 underground (UG) and very-low current configuration (VLCC) single-family or duplex residences, selected from a database of nearly 1000 residences specifically because their magnetic fields are most likely affected negligibly by overhead power lines. Using linear regression techniques, four factors predictive of the log-transformed residential field were identified: the square-root of the 24-h average net service drop current (this current is equivalent to the current in the grounding system), the log of the number of service drops on the same secondary serving the residence, residence age (four categories), and area type (rural, suburban, or urban). Complete data on ground current and service drops, the two factors with the strongest individual relationships to measured fields, were available for only half of the residences in the sample. However, these data were determined to be "missing at random" according to established statistical criteria. The full-sample or "composite" models thus relied on a method similar to regression imputation, accounting for missing data with binary dummy variables. When applied to the samples from which they were derived, these models accounted for 25% of the variance of the log-spot-measured magnetic field values in the full sample, while models that considered only those residences with complete data (n = 167) explained about 35%. The model validated well against a sample of 201 ordinary low current configuration (OLCC) homes selected from the same database.

Screening for cerebral aneurysm in patients with polycystic liver disease

BACKGROUND

Polycystic liver disease (PCLD) is an autosomal dominant disease characterized by multiple macrocystic lesions throughout the liver. The association between PCLD and cerebral aneurysm is well documented, and approximately 20% of patients with PCLD have demonstrable cerebral aneurysms at autopsy. The prevalence reported from autopsy series, however, may not reflect the true prevalence in patients with PCLD. We undertook this study to evaluate the prevalence and diagnosis of cerebral aneurysms in screening cerebral studies in patients with PCLD.

METHODS

Patients were identified by searching the hepatobiliary surgical service data base and hospital medical records. Hospital charts were reviewed to confirm presence of PCLD and to identify screening studies for cerebral aneurysms.

RESULTS

Ten patients with PCLD received screening studies of the cerebral vasculature during a 10 1/2-year period. One patient was found to have an asymptomatic cerebral aneurysm. A 45-year-old woman with no other significant medical history was referred for evaluation of PCLD. Screening magnetic resonance angiography (MRA) revealed a 5 mm aneurysm extending anteriorly near the origin of the right ophthalmic artery, without evidence of rupture. Cerebral angiography confirmed these findings, and the aneurysm was clipped.

CONCLUSIONS

Because cerebral aneurysms can be an important source of morbidity and mortality in PCLD, we recommend screening by MRA or by computed tomographic angiography (CTA) of the cerebral vasculature in all patients who have PCLD.

"The home infusion patient": patient profiles for the home infusion therapy market

The authors review the relevant literature regarding home health care patient profiles. An empirical analysis is provided from archival data for a home infusion company servicing patients in urban and rural areas. The results are provided as a 2 x 2 matrix for patients in urban and rural areas seeing either a specialist or primary care physicians. A series of moderated regressions indicate that type of treating physician, patient's gender, geographic residence and level of acuity are cogent in predicting the complexity of prescribed infusion therapies. Managerial implications are provided for the home care marketer in segmenting patient markets for infusion services.

Regulation of ribosome biogenesis by the rapamycin-sensitive TOR-signaling pathway in Saccharomyces cerevisiae

The TOR (target of rapamycin) signal transduction pathway is an important mechanism by which cell growth is controlled in all eucaryotic cells. Specifically, TOR signaling adjusts the protein biosynthetic capacity of cells according to nutrient availability. In mammalian cells, one branch of this pathway controls general translational initiation, whereas a separate branch specifically regulates the translation of ribosomal protein (r-protein) mRNAs. In Saccharomyces cerevisiae, the TOR pathway similarly regulates general translational initiation, but its specific role in the synthesis of ribosomal components is not well understood. Here we demonstrate that in yeast control of ribosome biosynthesis by the TOR pathway is surprisingly complex. In addition to general effects on translational initiation, TOR exerts drastic control over r-protein gene transcription as well as the synthesis and subsequent processing of 35S precursor rRNA. We also find that TOR signaling is a prerequisite for the induction of r-protein gene transcription that occurs in response to improved nutrient conditions. This induction has been shown previously to involve both the Ras-adenylate cyclase as well as the fermentable growth medium-induced pathways, and our results therefore suggest that these three pathways may be intimately linked.

Neisseria gonorrhoeae PilA is an FtsY homolog

The pilA gene of Neisseria gonorrhoeae was initially identified in a screen for transcriptional regulators of pilE, the expression locus for pilin, the major structural component of gonococcal pili. The predicted protein sequence for PilA has significant homology to two GTPases of the mammalian signal recognition particle (SRP), SRP54 and SRalpha. Homologs of SRP54 and SRalpha were subsequently identified in bacteria (Ffh and FtsY, respectively) and appear to form an SRP-like apparatus in prokaryotes. Of the two proteins, PilA is the most similar to FtsY (47% identical and 67% similar at the amino acid level). Like FtsY, PilA is essential for viability and hydrolyzes GTP. The similarities between PilA and the bacterial FtsY led us to ask whether PilA might function as the gonococcal FtsY. In this work, we show that overproduction of PilA in Escherichia coli leads to an accumulation of pre-beta-lactamase, similar to previous observations with other bacterial SRP components. Low-level expression of pilA in an ftsY conditional mutant can complement the ftsY mutation and restore normal growth to this strain under nonpermissive conditions. In addition, purified PilA can replace FtsY in an in vitro translocation assay using purified E. coli SRP components. A PilA mutant that is severely affected in its GTPase activity cannot replace FtsY in vivo or in vitro. However, overexpression of the GTPase mutant leads to the accumulation of pre-beta-lactamase, suggesting that the mutant protein may interact with the SRP apparatus to affect protein maturation. Taken together, these results show that the gonococcal PilA is an FtsY homolog and that the GTPase activity is necessary for its function.

Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor

The Ffh-4.5S ribonucleoprotein particle (RNP) and FtsY from Escherichia coli are homologous to essential components of the mammalian signal recognition particle (SRP) and SRP receptor, respectively. The ability of these E. coli components to function in a bona fide co-translational targeting pathway remains unclear. Here we demonstrate that the Ffh-4.5S RNP and FtsY can efficiently replace their mammalian counterparts in targeting nascent secretory proteins to microsomal membranes in vitro. Targeting in the heterologous system requires a hydrophobic signal sequence, utilizes GTP and, moreover, occurs co-translationally. Unlike mammalian SRP, however, the Ffh-4.5S RNP is unable to arrest translational elongation, which results in a narrow time window for the ribosome nascent chain to interact productively with the membrane-bound translocation machinery. The highly negatively charged N-terminal domain of FtsY, which is a conserved feature among prokaryotic SRP receptor homologs, is important for translocation and acts to localize the protein to the membrane. Our data illustrate the extreme functional conservation between prokaryotic and eukaryotic SRP and SRP receptors and suggest that the basic mechanism of co-translational protein targeting is conserved between bacteria and mammals.

A model of time-effective group psychotherapy for patients with personality disorders: the clinical model

This article describes a model of time-limited psychotherapy for patients with personality disorders that emphasizes the group as a social microcosm. The patient population described is relatively high functioning, although the majority of the group members meet DSM-III-R (American Psychiatric Association, 1987) criteria for an Axis II diagnosis. The clinical model's key theoretical concepts, for example, interpersonal focus; active therapist stance; emphasis on group interaction and processes; use of time limits; primary care/intermittent treatment philosophy; and emphasis on patients' strengths, goals, and resources are described. The relationships between the phases of group therapy and the key theoretical concepts are delineated.

Subfoveal neovascular membrane removal in patients with traumatic choroidal rupture

PURPOSE

To describe the clinical outcomes of patients undergoing pars plana vitrectomy to remove subretinal neovascular membranes caused by traumatic choroidal ruptures.

METHODS

Three patients with traumatic choroidal rupture in whom subfoveal choroidal neovascularization developed underwent pars plana vitrectomy with surgical excision of the neovascular membrane. Surgical specimens were examined histopathologically in two patients.

RESULTS

The choroidal neovascularization was removed completely in each patient. Visual results were excellent with visual acuities improving to 20/30 or better in each patient. Recurrence of choroidal neovascularization has not been observed. Fibrovascular membranes with reactive retinal pigment epithelium were observed in two specimens examined histopathologically.

CONCLUSION

Surgical removal of subretinal neovascular membranes emanating from traumatic choroidal ruptures produced an excellent visual outcome in three patients studied. The neovascular membranes, which were removed with minor disturbance to the underlying pigment epithelium, have similar characteristics to those obtained from patients with ocular histoplasmosis syndrome.

The nascent polypeptide-associated complex modulates interactions between the signal recognition particle and the ribosome

BACKGROUND

The first step in the co-translational targeting of secretory proteins to the endoplasmic reticulum membrane involves the recognition of signal sequences by the 54 kDa subunit of the signal recognition particle (SRP) as they emerge from the ribosome. It has recently been proposed that the nascent polypeptide-associated complex (NAC) contributes to the fidelity of targeting by modulating interactions that occur between the ribosome-nascent chain complex, the SRP and the endoplasmic reticulum membrane. Precisely how NAC influences SRP function is presently unclear.

RESULTS

We have used immunoblotting experiments to monitor interactions between the SRP and the ribosome-nascent chain complex, in the absence and presence of NAC. In the absence of NAC, SRP binds in a high-salt-resistant manner only to ribosomes that contain a signal sequence, confirming the specificity of SRP for signal sequences. Binding of SRP to signalless ribosome nascent chains is observed at lower salt concentrations; however, the amount of SRP bound to this complex is indistinguishable from that bound to ribosomes lacking nascent chains. Thus, this salt-sensitive binding is likely to be the result of interactions between SRP and the ribosome that occur independently of the nascent chain. A minimal particle consisting of SRP54 and SRP RNA is sufficient to confer salt-resistant binding to ribosomes that contain signal sequences, whereas all of the SRP subunits are required for salt-sensitive binding to ribosomes that lack nascent chains. This salt-sensitive binding by SRP is inhibited by the addition of purified NAC.

CONCLUSIONS

Based on our results, we define two distinct modes of interaction between SRP and the ribosome-nascent chain complex: salt-resistant interactions between SRP54 and signal sequences, and salt-sensitive interactions between additional components of SRP and the ribosome. We conclude that NAC does not directly influence signal sequence recognition by SRP but, rather, that it negatively modulates interactions that occur between SRP and the ribosome itself. These results are discussed in terms of a model wherein SRP and NAC regulate each others' activity during protein targeting.

Analysis of the practice of nutrition support pharmacy specialists

In 1988 the Board of Pharmaceutical Specialities (BPS) recognized nutrition support pharmacy practice (NSPP) as one of four specialty areas in pharmacy. The BPS appointed a specialty council to develop and manage the process for board certification of qualified specialists. One step was to identify and validate activities performed by the specialists. This was accomplished by conducting a study that delineated the role of these practitioners and also provided information for developing a blueprint for a certification examination. The results revealed the types of practice settings, education, and training for specialists, and the distribution of professional time devoted to nutrition support activities.

Reciprocal stimulation of GTP hydrolysis by two directly interacting GTPases

The Escherichia coli guanosine triphosphate (GTP)-binding proteins Ffh and FtsY have been proposed to catalyze the cotranslational targeting of proteins to the bacterial plasma membrane. A mutation was introduced into the GTP-binding domain of FtsY that altered its nucleotide specificity from GTP to xanthosine triphosphate (XTP). The mutant FtsY protein stimulated GTP hydrolysis by a ribonucleoprotein consisting of Ffh and 4.5S RNA in a reaction that required XTP, and it hydrolyzed XTP in a reaction that required both the Ffh-4.5S ribonucleoprotein and GTP. Thus, nucleotide triphosphate hydrolysis by Ffh and FtsY is likely to occur in reciprocally coupled reactions in which the two interacting guanosine triphosphatases act as regulatory proteins for each other.

Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA

Complexes between 16S rRNA and purified ribosomal proteins, either singly or in combination, were assembled in vitro and probed with hydroxyl radicals generated from free Fe(II)-EDTA. The broad specificity of hydroxyl radicals for attack at the ribose moiety in both single- and double-stranded contexts permitted probing of nearly all of the nucleotides in the 16S rRNA chain. Specific protection of localized regions of the RNA was observed in response to assembly of most of the ribosomal proteins. The locations of the protected regions were in good general agreement with the footprints previously reported for base-specific chemical probes, and with sites of RNA-protein crosslinking. New information was obtained about interaction of ribosomal proteins with 16S rRNA, especially with helical elements of the RNA. In some cases, 5' or 3' stagger in the protection pattern on complementary strands suggests interaction of proteins with the major or minor groove, respectively, of the RNA. These results reinforce and extend previous data on the localization of ribosomal proteins with respect to structural features of 16S rRNA, and offer many new constraints for three-dimensional modeling of the 30S ribosomal subunit.

A temperature-dependent conformational rearrangement in the ribosomal protein S4.16 S rRNA complex

Ribosomal protein S4 protects a characteristic set of bases in 16 S rRNA from attack by chemical probes. Use of hydroxyl radical as a probe of the RNA backbone shows that ribose residues in these same regions are also protected by S4, confirming the localization of its interactions with 16 S rRNA to the junction of five helical elements in the proximal region of the 5' domain. At 0 degrees C, the nucleotides protected by S4 from base-specific probes are confined almost exclusively to the two compound helices formed by residues 404-499. After subsequent heating of the complex briefly at 30 or 42 degrees C, nucleotides in the three adjacent helices are additionally protected, resulting in a pattern of protection that is identical to that which is observed when S4 is incubated with 16 S rRNA under in vitro reconstitution conditions. Preincubation of the protein or the RNA (or both) separately at elevated temperature does not substitute for heating the S4.RNA complex. The regions in the RNA affected by the heat step are known to interact with proteins S12 and S16, both of which depend upon S4 for their binding to the RNA. Thus, the finding that S4 recruits additional sites of interaction in the RNA following its initial binding suggests a possible mechanism to insure the sequential addition of proteins during ribosomal assembly.

Intratracheal pulmonary ventilation (ITPV): control of positive end-expiratory pressure at the level of the carina through the use of a novel ITPV catheter design

A new mode of pulmonary ventilation called intratracheal pulmonary ventilation (ITPV) was studied. Briefly, a continuous flow of air/oxygen is introduced through a small catheter, the tip of which is positioned at the carina, with a diffuser mounted at its distal end. A timed expiration valve, when closed, provides for inspiration; when open, it provides for expiration. The system as first described had a potential for significant back pressure at the level of the carina, which was more at rapid gas flows and with smaller endotracheal tubes. We have now mounted a venturi on the tip of the catheter (reverse thrust catheter [RTC]) that avoids back pressure, and which facilitates expiration. At respiratory rates from 10 to 120/min, the ITPV system with the RTC maintained end-expiratory pressure at the level of the carina at, or near 0 cm H2O. Compared to conventional mechanical ventilation, at identical respiratory rates, this system reduced tidal volume by one half at the lowest respiratory rates, and by as much as two thirds at the highest respiratory rates, with a proportional decrease in peak inspiratory pressure. ITPV has the smallest minute volume ventilation of any conventional or nonconventional mode of pulmonary ventilation.

Comparison of diode and argon laser trabeculoplasty in cadaver eyes

PURPOSE

To evaluate differences in the effects of diode and argon trabeculoplasty on cadaver eye trabecular meshwork.

METHODS

The argon laser was used at a 50 mu spot size, 500 to 100 mW of power, and a 0.1 second time interval, and the diode laser was used at a 0.1 to 0.2 second time interval, 100 mu spot size, and 400 to 1200 mW of power. Analysis was performed using videography, microscopy, and scanning electron microscopy.

RESULTS

This study found grossly that burns with the argon laser caused tissue blanching and pigment dispersion, whereas no reaction was observed with the diode laser. The diode laser made no observable histologic alterations, but the argon caused fragmentation and coagulation of trabecular beams. Scanning electron microscopy showed that the diode laser caused an area of trabecular beam coalescence measuring 50 to 100 mu in diameter with energies > or = 0.12 J. A surrounding zone of more superficial trabecular beam fragmentation measuring 200 to 400 mu in diameter also was observed. Similar energy levels from the argon laser caused hole formation 200 to 400 mu in diameter. Lower argon energy levels (0.05 J) caused inconsistent coalescence 50 to 100 mu in diameter similar to the diode laser.

CONCLUSIONS

This study suggests that in the trabecular meshwork the diode laser causes a reaction at, but not at less than, energy levels shown previously to produce a clinical ocular hypotensive effect. Also, at similar energy per area, the tissue effects of the diode and argon laser are comparable.

Selective perturbation of G530 of 16 S rRNA by translational miscoding agents and a streptomycin-dependence mutation in protein S12

Previous studies have shown that a concise set of universally conserved bases in 16 S rRNA are strongly protected from attack by chemical probes when tRNA is bound specifically to the ribosomal A site. Two of these bases, A1492 and A1493, are located in the cleft of the 30 S subunit, the site of codon-anticodon interaction. A third residue, G530, is located within the highly conserved 530 stem-loop, a region that is involved in interactions with proteins S4 and S12, mutations in which perturb the translational error frequency. The 530 loop is also thought to be located at or near the site of interaction of elongation factor Tu on the 30 S subunit, a location that is distinct from the decoding site. This study monitors the response of these two A-site-related regions of 16 S rRNA to a variety of translational miscoding agents. Several of these agents, including streptomycin, neomycin and ethanol, selectively potentiate tRNA-dependent protection of residue G530 from kethoxal modification; in contrast, little change in reactivity of residues A1492 and A1493 is observed. These results are consistent with the previously demonstrated importance of G530 for A-site function and, moreover, suggest a common mechanism of action for these miscoding agents, even though they appear to have distinctly different modes of interaction with 16 S rRNA. In contrast to the miscoding agents, we find that a streptomycin-dependence (SmD) mutation in protein S12, which causes ribosomes to be hyperaccurate, antagonizes tRNA-dependent protection of G530. The possibility that 5' or 3' flanking regions of mRNA could be involved in tRNA-dependent protection of G530 was tested by using different lengths of oligo(U) to promote binding of tRNA(Phe) to the A site. The relative levels of protection of G530, A1492 and A1493 were unchanged as the size of the mRNA fragment was decreased from 16 to 6 bases in length. We conclude, therefore, that for protection of G530 to be the result of direct contact with message, it must necessarily be located directly at the decoding site; otherwise, its protection is best explained by allosteric interactions, either with mRNA, or with the codon-anticodon complex. These results are discussed in terms of a model wherein the conformation of the 530 loop is correlated with the affinity of the ribosome for elongation factor Tu.

The 530 loop of 16S rRNA: a signal to EF-Tu?

The molecular mechanism of tRNA selection has remained elusive. Recent evidence, both biochemical and genetic, suggests the involvement of 'smart' ribosomes, that can signal the elongation factor Tu by way of conformational changes in ribosomal RNA.

Anophthalmic socket pain

We examined and treated four patients with anophthalmic socket pain. Conditions responsible for this problem in this series included scleritis after evisceration, amputation neuroma, pain from a skull-base meningioma, and chemical dependency with drug-seeking behavior. The pain associated with the scleritis after evisceration responded to removal of the scleral remnant. The pain associated with the amputation neuroma responded to removal of the orbital implant and its pseudocapsule in which the amputation neuroma was embedded. The pain associated with the meningioma was intractable. The pain associated with the chemical dependency remained a persistent problem. A careful history and physical examination are critical in the evaluation of anophthalmic socket pain. Computed tomography or magnetic resonance imaging may be helpful in some cases.

Dynamics of in vitro assembly of 16 S rRNA into 30 S ribosomal subunits

One of the important unsolved problems in the ribosome field is the molecular basis for the sequential and co-operative nature of ribosome assembly. As an approach to this problem, we have taken advantage of the temperature dependence of in vitro reconstitution and have used chemical probing methods to examine the conformation and reactivity of 16 S rRNA at successive stages during subunit assembly. One class of nucleotides displays reactivities similar to those observed in native 30 S particles when the RNA and protein are incubated in the absence of any heat step (0 degrees C effects). At 30 degrees C, where the assembly process takes 2 hours, other bases can be assigned to one of several additional kinetic classes, determined by the rate at which their chemical reactivities transit from levels observed in naked RNA to levels observed in fully assembled subunits: (1) fast (t1/2 = < 5 min at 30 degrees C); (2) slow (t1/2 = 15 to 30 min at 30 degrees C); (3) delayed slow (t1/2 = 30 to 60 min at 30 degrees C). Finally, several nucleotides display transient kinetics in their reactivities, showing increasing reactivity at early time points and becoming protected later in assembly; most of these effects correspond to residues that were previously shown to display reciprocal enhancement and protection patterns during step-wise in vitro assembly. These findings, together with our previous studies using purified individual proteins lead to the following conclusions: (1) there is a predominant 5' to 3' polarity to in vitro assembly, even though it is uncoupled from transcription; (2) portions of the central and 3' major domains fold into an active conformation only at a very late stage of assembly; (3) bases footprinted by late-assembling proteins, according to the 30 S subunit assembly map, show generally slower kinetics than residues footprinted by proteins that bind early in the assembly map, providing direct evidence for the sequential nature of the in vitro assembly process; (4) most proteins are associated with nucleotides that fall into more than one kinetic class, suggesting that assembly proceeds through multiple pathways, or that individual proteins interact sequentially with different regions of the RNA.

Evidence for functional interaction between elongation factor Tu and 16S ribosomal RNA

Translation of the genetic code requires the accurate selection of elongation factor (EF)-Tu.GTP.tRNA ternary complexes at the ribosomal acceptor site, or A site. Several independent lines of evidence have implicated the universally conserved 530 loop of 16S rRNA in this process; yet its precise role has not been identified. Using an allele-specific chemical probing strategy, we have examined the functional defect caused by a dominant lethal G-->A substitution at position 530. We find that mutant ribosomes are impaired in EF-Tu-dependent binding of aminoacyl-tRNA in vitro; in contrast, nonenzymatic binding of tRNA to the A and P sites is unaffected, indicating that the defect involves an EF-Tu-related function rather than tRNA-ribosome interactions per se. In vivo, the mutant ribosomes are found in polysomes at low levels and contain reduced amounts of A-site-bound tRNA, but normal levels of P-site tRNA, in agreement with the in vitro results; thus the dominant lethal phenotype of mutations at G530 can be explained by impaired interaction of mutant ribosomes with ternary complex. These results provide evidence for a newly defined function of 16S rRNA--namely, modulation of EF-Tu activity during translation.

Allele-specific structure probing of plasmid-derived 16S ribosomal RNA from Escherichia coli

Biochemical analysis of Escherichia coli ribosomes containing mutant 16S or 23S (r)ribosomal RNAs, produced via cloned rDNA genes on multicopy plasmids, has been hindered by the background of wild-type (wt) ribosomes containing host-derived rRNA. Here, we describe a method for the construction of unique priming sites in 16S rRNA that allow allele-specific structure probing of ribosomes containing plasmid-encoded RNA. Phenotypically silent mutations, designed to mimic related eubacterial sequences, have been introduced into four phylogenetically variable regions in the 16S rDNA gene that allow inspection of several 16S rRNA functional sites. When oligodeoxyribonucleotides complementary to these altered sequences are used to prime cDNA synthesis in primer extension reactions using reverse transcriptase, only plasmid-derived 16S rRNA is used as a template, thus rendering the wt background invisible. Unexpectedly, we were unable to introduce silent mutations into one nonconserved helix in 16S rRNA, suggesting that constraints in addition to Watson-Crick pairing are important in this region.

Specific structural probing of plasmid-coded ribosomal RNAs from Escherichia coli

The preferred method for construction and in vivo expression of mutagenised Escherichia coli ribosomal RNAs (rRNAs) is via high copy number plasmids. Transcription of wild-type rRNA from the seven chromosomal rrn operons in strains harbouring plasmid-coded mutant rRNAs leads to a heterogeneous ribosome population, which consequently hinders direct probing of mutant rRNAs. Here, we describe how nonconserved helical regions of plasmid-coded rRNA have been altered in a manner that preserves their secondary structures while creating new sites for primer extension of mutant rRNAs. This facilitates specific biochemical probing of mutagenised rRNA regions despite the background of wild-type molecules. Four priming sites have been made to investigate the structural effects of mutations in the GTPase centre, helix 1200-1250, the peptidyl transferase region and the alpha-sarcin loop of 23S rRNA.

A functional pseudoknot in 16S ribosomal RNA

Several lines of evidence indicate that the universally conserved 530 loop of 16S ribosomal RNA plays a crucial role in translation, related to the binding of tRNA to the ribosomal A site. Based upon limited phylogenetic sequence variation, Woese and Gutell (1989) have proposed that residues 524-526 in the 530 hairpin loop are base paired with residues 505-507 in an adjoining bulge loop, suggesting that this region of 16S rRNA folds into a pseudoknot structure. Here, we demonstrate that Watson-Crick interactions between these nucleotides are essential for ribosomal function. Moreover, we find that certain mild perturbations of the structure, for example, creation of G-U wobble pairs, generate resistance to streptomycin, an antibiotic known to interfere with the decoding process. Chemical probing of mutant ribosomes from streptomycin-resistant cells shows that the mutant ribosomes have a reduced affinity for streptomycin, even though streptomycin is thought to interact with a site on the 30S subunit that is distinct from the 530 region. Data from earlier in vitro assembly studies suggest that the pseudoknot structure is stabilized by ribosomal protein S12, mutations in which have long been known to confer streptomycin resistance and dependence.

A nutrition support team quality assurance plan

The Nutrition Support Team at the Veterans Affairs Medical Center is responsible for the development of guidelines related to the provision of both total parenteral nutrition and enteral nutrition support. A Quality Assurance plan which was approved by the Joint Commission on Accreditation of HealthCare Organizations was implemented by the Nutrition Support Team. This plan addresses: nutritional assessment and consultation, indications for enteral and parenteral nutrition support, provision of optimal nutrition support including attainment of nutritional goals, and the prevention, detection, and management of complications. The indicators and criteria for each aspect of care are described. This program has provided documentation of the activities of the Nutrition Support Team as well as data defining the patient population requiring specialized nutrition support, and has helped identify areas where improvement is required.

Prospective randomized evaluation of two regimens for converting from continuous to intermittent feedings in patients with feeding gastrostomies

Forty enterally fed male patients were randomized to one of two regimens designed to determine the better means of converting them from continuous to intermittent enteral feedings. All patients received a nutritionally complete iso-osmolal 1 kcal/cc formula containing 6 g of nitrogen/L beginning on the second postgastrostomy day. Half of the patients (20) were randomized to a discontinuous regimen abruptly changing from continuous to gradually increasing intermittent feedings until reaching their nutritional goals. Intravenous fluids were given to maintain normal fluid balance. The other 20 patients were randomized to an overlapping regimen, receiving continuous feedings at a decreasing rate while intermittent feedings were progressively increased. Intravenous fluids were used during the first three stages only. There were no significant differences (p less than 0.05) in major diagnosis, type of gastrostomy, age, weight, height, admission or discharge serum albumin concentration, calculated basal energy expenditure (BEE), or nutrient goals (1.5 X BEE, 1.5 g of protein/kg per day).(ABSTRACT TRUNCATED AT 250 WORDS)

Clinical and economic effect of ciprofloxacin as an alternative to injectable antimicrobial therapy

The effect of the use of oral ciprofloxacin on patient outcome and the cost of antimicrobial therapy was investigated. In 1988 ciprofloxacin was placed on the antimicrobial formulary at a Veterans Affairs medical center. Patients with urinary tract infections, soft tissue infections, osteomyelitis, or pneumonia due to organisms that were documented as being susceptible to ciprofloxacin and either resistant to other oral antimicrobials or susceptible to other oral antimicrobials in patients allergic to such agents were monitored in a prospective open study over 12 months. When a patient was enrolled, the physician was asked to select the i.v. antimicrobial regimen that would have been used if ciprofloxacin were not available. Patient outcome was determined from medical records, and the difference in the costs of the oral and i.v. regimens was calculated. Clinical cure occurred in 96/100 (96%) of patients with urinary tract infection, 19/22 (86%) with soft tissue infection, 14/16 (88%) with osteomyelitis, and 10/12 (83%) with pneumonia. The overall cure rate was 139/150 (93%). The 11 clinical failures occurred in patients infected with methicillin-resistant Staphylococcus aureus (MRSA) alone, group D enterococcus alone, MRSA and Pseudomonas sp., and Pseudomonas sp. alone. The total cost avoidance achieved by using oral ciprofloxacin instead of i.v. antimicrobials was $77,158. Oral ciprofloxacin was an effective and cost-efficient alternative to traditional i.v. antimicrobial therapy in the patients studied.

Defining the structural requirements for a helix in 23 S ribosomal RNA that confers erythromycin resistance

The helix spanning nucleotides 1198 to 1247 (helix 1200-1250) in Escherichia coli 23 S ribosomal RNA (rRNA) is functionally important in protein synthesis, and deletions in this region confer erythromycin resistance. In order to define the structural requirements for resistance, we have dissected this region using in vitro mutagenesis. Erythromycin resistance is established after a minimal deletion of three bases, CAU1231 or AUG1232. The maximum deletion observed to confer resistance is 25 bases. The level of erythromycin resistance conferred by intermediate sized deletions is variable and some deletion mutants show a sensitive phenotype. Deletions that extend into the base-pairing between GCC1208 and GGU1240 result in non-functional 23 S RNAs, which consequently do not confer resistance. A number of phylogenetically conserved nucleotides have been shown to be non-essential for 23 S RNA function. However, removal of either these or non-conserved nucleotides from helix 1200-1250 measurably reduces the efficiency of 23 S RNA in forming functional ribosomes. We have used chemical probing and a modified primer extension method to investigate erythromycin binding to wild-type and resistant ribosomes with a 12-base deletion in 23 S RNA. Erythromycin interacts as strongly with mutant 23 S RNA as with wild-type 23 S RNA. Deletions in the 1200-1250 helix do not therefore confer resistance by reducing erythromycin binding, but by suppressing the effects of the drug at the level of its mechanism of action.

RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA

Chemical probing methods have been used to "footprint" 16S ribosomal RNA (rRNA) at each step during the in vitro assembly of twenty 30S subunit ribosomal proteins. These experiments yield information about the location of each protein relative to the structure of 16S rRNA and provide the basis for derivation of a detailed model for the three-dimensional folding of 16S rRNA. Several lines of evidence suggest that protein-dependent conformational changes in 16S rRNA play an important part in the cooperativity of ribosome assembly and in fine-tuning of the conformation and dynamics of 16S rRNA in the 30S subunit.

Interaction of ribosomal proteins S5, S6, S11, S12, S18 and S21 with 16 S rRNA

We have examined the effects of assembly of ribosomal proteins S5, S6, S11, S12, S18 and S21 on the reactivities of residues in 16 S rRNA towards chemical probes. The results show that S6, S18 and S11 interact with the 690-720 and 790 loop regions of 16 S rRNA in a highly co-operative manner, that is consistent with the previously defined assembly map relationships among these proteins. The results also indicate that these proteins, one of which (S18) has previously been implicated as a component of the ribosomal P-site, interact with residues near some of the recently defined P-site (class II tRNA protection) nucleotides in 16 S rRNA. In addition, assembly of protein S12 has been found to result in the protection of residues in both the 530 stem/loop and the 900 stem regions; the latter group is closely juxtaposed to a segment of 16 S rRNA recently shown to be protected from chemical probes by streptomycin. Interestingly, both S5 and S12 appear to protect, to differing degrees, a well-defined set of residues in the 900 stem/loop and 5'-terminal regions. These observations are discussed in terms of the effects of S5 and S12 on streptomycin binding, and in terms of the class III tRNA protection found in the 900 stem of 16 S rRNA. Altogether these results show that many of the small subunit proteins, which have previously been shown to be functionally important, appear to be associated with functionally implicated segments of 16 S rRNA.

Probing the assembly of the 3' major domain of 16 S rRNA. Interactions involving ribosomal proteins S2, S3, S10, S13 and S14

We have used rapid probing methods to follow the changes in reactivity of residues in 16 S rRNA to chemical and enzymatic probes as ribosomal proteins S2, S3, S10, S13 and S14 are assembled into 30 S subunits. Effects observed are confined to the 3' major domain of the RNA and comprise three general classes. (1) Monospecific effects, which are attributable to a single protein. Proteins S13 and S14 each affect the reactivities of different residues which are adjacent to regions previously found protected by S19. S10 effects are located in two separate regions of the domain, the 1120/1150 stem and the 1280 loop; both of these regions are near nucleotides previously found protected by S9. Both S2 and S3 protect different nucleotides between positions 1070 and 1112. In addition, S2 protects residues in the 1160/1170 stem-loop. (2) Co-operative effects, which include residues dependent on the simultaneous presence of both proteins S2 and S3 for their reactivities to appear similar to those observed in native 30 S subunits. (3) Polyspecific effects, where proteins S3 and S2 independently afford the same protection and enhancement pattern in three distal regions of the domain: the 960 stem-loop, the 1050/1200 stem and in the upper part of the domain (nucleotides 1070 to 1190). Proteins S14 and S10 also weakly affect the reactivities of several residues in these regions. We believe that several of the protected residues of the first class are likely sites for protein-RNA contact while the third class is indicative of conformational rearrangement in the RNA during assembly. These results, in combination with the results from our previous study of proteins S7, S9 and S19, are discussed in terms of the assembly, topography and involvement in ribosomal function of the 3' major domain.

Probing the assembly of the 3' major domain of 16 S ribosomal RNA. Quaternary interactions involving ribosomal proteins S7, S9 and S19

We have studied the effect of assembly of ribosomal proteins S7, S9 and S19 on the accessibility and conformation of nucleotides in 16 S ribosomal RNA. Complexes formed between 16 S rRNA and S7, S7 + S9, S7 + S19 or S7 + S9 + S19 were subjected to a combination of chemical and enzymatic probes, whose sites of attack in 16 S rRNA were identified by primer extension. The results of this study show that: (1) Protein S7 affects the reactivity of an extensive region in the lower half of the 3' major domain. Inclusion of proteins S9 or S19 with S7 has generally little additional effect on S7-specific protection of the RNA. Clusters of nucleotides that are protected by protein S7 are localized in the 935-945 region, the 950/1230 stem, the 1250/1285 internal loop, and the 1350/1370 stem. (2) Addition of protein S9 in the presence of S7 causes several additional effects principally in two structurally distal regions. We observe strong S9-dependent protection of positions 1278 to 1283, and of several positions in the 1125/1145 internal loop. These findings suggest that interaction of protein S9 with 16 S rRNA results in a structure in which the 1125/1145 and 1280 regions are proximal to each other. (3) Most of the strong S19-dependent effects are clustered in the 950-1050 and 1210-1230 regions, which are joined by base-pairing in the 16 S rRNA secondary structure. The highly conserved 960-975 stemp-loop, which has been implicated in tRNA binding, appears to be destabilized in the presence of S19. (4) Protein S7 causes enhanced reactivity at several sites that become protected upon addition of S9 or S19. This suggests that S7-induced conformational changes in 16 S rRNA play a role in the co-operativity of assembly of the 3' major domain.