Delirium detection tools show varying completion rates and positive score rates when used at scale in routine practice in general hospital settings: A systematic review

BACKGROUND

Multiple short delirium detection tools have been validated in research studies and implemented in routine care, but there has been little study of these tools in real-world conditions. This systematic review synthesized literature reporting completion rates and/or delirium positive score rates of detection tools in large clinical populations in general hospital settings.

METHODS

PROSPERO (CRD42022385166). Medline, Embase, PsycINFO, CINAHL, and gray literature were searched from 1980 to December 31, 2022. Included studies or audit reports used a validated delirium detection tool performed directly with the patient as part of routine care in large clinical populations (n ≥ 1000) within a general acute hospital setting. Narrative synthesis was performed.

RESULTS

Twenty-two research studies and four audit reports were included. Tools used alone or in combination were the Confusion Assessment Method (CAM), 4 'A's Test (4AT), Delirium Observation Screening Scale (DOSS), Brief CAM (bCAM), Nursing Delirium Screening Scale (NuDESC), and Intensive Care Delirium Screening Checklist (ICDSC). Populations and settings varied and tools were used at different stages and frequencies in the patient journey, including on admission only; inpatient, daily or more frequently; on admission and as inpatient; inpatient post-operatively. Tool completion rates ranged from 19% to 100%. Admission positive score rates ranged from: CAM 8%-51%; 4AT 13%-20%. Inpatient positive score rates ranged from: CAM 2%-20%, DOSS 6%-42%, and NuDESC 5-13%. Postoperative positive score rates were 21% and 28% (4AT). All but two studies had moderate-high risk of bias.

CONCLUSIONS

This systematic review of delirium detection tool implementation in large acute patient populations found clinically important variability in tool completion rates, and in delirium positive score rates relative to expected delirium prevalence. This study highlights a need for greater reporting and analysis of relevant healthcare systems data. This is vital to advance understanding of effective delirium detection in routine care.

Predictors of post-stroke cognitive impairment using acute structural MRI neuroimaging: A systematic review and meta-analysis

BACKGROUND

Stroke survivors are at an increased risk of developing post-stroke cognitive impairment and post-stroke dementia; those at risk could be identified by brain imaging routinely performed at stroke onset.

AIM

This systematic review aimed to identify features which are associated with post-stroke cognitive impairment (including dementia) on magnetic resonance imaging (MRI) performed at stroke diagnosis.

SUMMARY OF REVIEW

We searched the literature from inception to January 2022 and identified 10,284 records. We included studies that performed MRI at the time of stroke (0-30 days after a stroke) and assessed cognitive outcome at least 3 months after stroke. We synthesized findings from 26 papers, comprising 27 stroke-populations (N = 13,114, average age range = 40-80 years, 19-62% female). When data were available, we pooled unadjusted (OR_u) and adjusted (OR_a) odds ratios.We found associations between cognitive outcomes and presence of cerebral atrophy (three studies, N = 453, OR_u = 2.48, 95% CI = 1.15-4.62), presence of microbleeds (two studies, N = 9151, OR_a = 1.36, 95% CI = 1.08-1.70), and increasing severity of white matter hyperintensities (three studies, N = 704, OR_a = 1.26, 95% CI = 1.06-1.49). Increasing cerebral small vessel disease score was associated with cognitive outcome following unadjusted analysis only (two studies, N = 499, OR_u = 1.34, 95%CI = 1.12-1.61; three studies, N = 950, OR_a = 1.23, 95% CI = 0.96-1.57). Associations remained after controlling for pre-stroke cognitive impairment. We did not find associations between other stroke features and cognitive outcome, or there were insufficient data.

CONCLUSION

Acute stroke MRI features may enable healthcare professionals to identify patients at risk of post-stroke cognitive problems. However, there is still substantial uncertainty about the prognostic utility of acute MRI for this.

Nivolumab induced pulmonary sarcoid-like granulomas with a concurrent pleural schwannoma: A pathologic-radiologic correlation of a rare condition mimicking metastatic melanoma

Nivolumab is an anti-PD-1 antibody. The mechanism of action of nivolumab is inhibition of binding between PD-1 and PD-1 ligand. This causes activation of antigen-specific T cells that were previously unresponsive to cancer cells. This unique mechanism of action attributes the widespread use of nivolumab for the treatment of a variety of neoplastic conditions. On the other hand, this mode of action is associated with adverse effects as well. Schwannoma, also called neurilemmoma, is a benign peripheral nerve sheath tumor. Pleural schwannomas are very rare and very few cases have been reported in the medical English literature so far. Herein, we report a very rare case of concurrent presence of Nivolumab induced pulmonary sarcoid-like granulomas along with primary benign pleural schwannoma in a 49-year-old male. He was diagnosed with malignant melanoma of the right upper arm for which he underwent surgery and was receiving adjuvant chemotherapy. He developed pneumonitis during chemotherapy, and on imaging multiple reticular and nodular interstitial infiltrates were seen along with an incidental pleural mass with a high suspicion for metastasis. Wedge biopsy of the interstitial infiltrates was done and they were found to be pulmonary granulomas related to the nivolumab therapy he was receiving. The patient underwent excision of the pleural mass which showed histopathological and immunohistochemical features of schwannoma. The two conditions are unrelated and rarely encountered simultaneously. The radiologic and pathologic correlation along with differential diagnosis of these conditions are discussed.

Predicting post-stroke cognitive impairment using acute CT neuroimaging: A systematic review and meta-analysis

Background

Identifying whether acute stroke patients are at risk of cognitive decline could improve prognostic discussions and management. Structural computed tomography neuroimaging is routine in acute stroke, and may identify those at risk of post-stroke dementia or post-stroke cognitive impairment (PSCI).

Aim

To systematically review the literature to identify which stroke or pre-stroke features on brain computed tomography scans, performed at the time of stroke, are associated with post-stroke dementia or PSCI.

Summary of review

We searched electronic databases to December 2020. We included studies reporting acute stroke brain computed tomography, and later diagnosis of a cognitive syndrome. We created summary estimates of size of unadjusted association between computed tomography features and cognition. Of 9536 citations, 28 studies (41 papers) were eligible (N = 7078, mean age 59.8–78.6 years). Cognitive outcomes were post-stroke dementia (10 studies), PSCI (17 studies), and one study analyzed both. Fifteen studies (N = 2952) reported data suitable for meta-analyses. White matter lesions (WML) (six studies, N = 1054, OR = 2.46, 95% CI = 1.25–4.84), cerebral atrophy (four studies, N = 558, OR = 2.80, 95% CI = 1.21–6.51), and pre-existing stroke lesions (three studies, N = 352, OR = 2.38, 95% CI = 1.06–5.32) were associated with post-stroke dementia. WML (four studies, N = 473, OR = 3.46, 95% CI = 2.17–5.52) were associated with PSCI. Other computed tomography features were either not associated with cognitive outcome, or there were insufficient data.

Conclusions

Cognitive impairment following stroke is of great concern to patients and carers. Features seen on visual assessment of acute stroke computed tomography brain scans are strongly associated with cognitive outcomes. Clinicians should consider when and how this information should be discussed with stroke survivors.

Lessons from recent medical history: an obsolete anti-reflux device in an older patient with variable gastrointestinal symptoms

A frail 93-year-old lady presented with delirium, on a background of heart failure, cerebrovascular disease, constipation and osteoporosis. A computed tomography (CT) pulmonary angiography, undertaken due to persistent hypoxia, identified no pathology aside from an unusual appearance of the left hypochondrium, necessitating further elucidation with CT abdomen. This unexpectedly reported the presence of a gastric band, leading us to consider possible misidentification. Perusing her General Practitioner (GP) records demonstrated that she underwent surgical insertion of an Angelchik prosthesis in 1984. Angelchik prostheses were anti-reflux devices used for a short period, before falling from favour due to increasing evidence around late developing complications. A collateral history from family revealed that this patient had experienced multiple longstanding symptoms including bloating, reflux and constipation, potentially linked to her prosthesis, a previously unestablished link.

125 A Case of Mistaken Identity: An Obsolete Anti-Reflux Device in An Older Patient with Variable Gastrointestinal Symptoms

Background

A frail 93-year-old lady presented with delirium and hypoxia, on a background of heart failure, constipation, cerebrovascular disease, and osteoporosis. A CTPA on admission revealed an unusual appearance of the left hypochondrium, leading to subsequent CT abdomen. This unexpectedly reported the presence of a gastric band. We therefore considered a possible misidentification as this procedure seemed unlikely in someone of her age. Her GP records revealed that she underwent surgical insertion of an Angelchik prosthesis in 1984. It transpired that our patient had experienced several longstanding symptoms, including reflux, bloating and constipation, which have all been observed in patients with Angelchik prostheses in situ.

Discussion

The Angelchik prosthesis is an anti-reflux device for patients with chronic reflux disease with or without hiatus hernia, introduced in 1979. It comprised of an elastomer shell ring filled with silicone gel, that was sited at the lower oesophagus and secured with DACRON tapes. It was initially lauded for its replicable insertion technique and promising early results with around 30,000 being inserted in mainly British and American Hospitals. However, over time it became apparent that a significant proportion of patients reported ongoing gastrointestinal symptoms due to device failure.

Serious complications such as gastric perforations were also recognised. Surgical removal was noted to be technically complex, providing further challenges. The Angelchik prosthesis therefore fell from favour after a period of use of only fifteen years, and is now rarely encountered. We discovered that our patient had experienced multiple long-standing gastrointestinal complaints potentially linked to her prosthesis, though this association had not previously been considered. Whilst her frailty meant that removal would not be pragmatic, it is uncertain if this could have been a possible consideration in the past. This device is relevant to geriatricians as many recipients are now elderly, and may report ongoing symptoms.

Une approche théorico-clinique des TCA et de la maternité

Résumé non reçu.

Extra-framework cation release from heulandite-type rich tuffs on exchange with NH(4)(+)

The outgoing cations of Greek heulandite-rich tuff samples (heulandite type-III, 91wt.%, mica 4wt.%, feldspar 5wt. %, CEC 2.22meq/g) were analysed upon exchange with ammonium acetate using atomic absorption spectrometry (AAS). The kinetic curves of each cation were investigated over a total time of contact of 720h with sampling at frequent intervals. The materials were examined by powder X-ray diffraction, SEM-EDS, and AAS. The sorption ability was measured using the ammonium acetate saturation method. It was found that Ca(2+) presents an unexpected extra-framework release and a surprisingly high degree of exchange (90%). The exchange of Mg (57%) is also worthy of note whereas the behavior of K(+) showed an expected rapid initial release. The behavior of Na(+) must be similar. However, its lower concentration in the zeolitic material minimizes its overall significance somewhat. On the other hand, Ca(2+) and Mg(2+) release is kinetically much slower, compared to that of alkali metal ions, and this phenomenon indicates that different exchange energies are needed till final equilibrium.

Use of autologous blood as part of the perfusate for cardiopulmonary bypass: a priming technique

In an attempt to replace the oncotic and protein coating capabilities of serum albumin in the perfusate, we established a priming protocol that used autologous blood as part of the perfusate solution. Prior to March 1, 1999, our standard priming protocol was 1650 ml of crystalloid with 250 ml of 5% serum albumin and 5,000 units of heparin. After removing albumin from our prime, our standard protocol was altered to include 40 ml of the patient's autologous blood in 1,800 ml of crystalloid and 10,000 units of heparin. To determine the intraoperative effects of using albumin/crystalloid primes (Group A), autologous blood/crystalloid primes (Group B) and crystalloid primes (Group C), a total of 178 patients were sequentially evaluated. Intraoperative parameters evaluated were total protein (TP), colloid osmotic pressure (COP), platelets (Plts) and fluid requirements during cardiopulmonary bypass (CPB). During an overlapping 12-month period of time, 1,092 consecutive cardiac surgical cases using CPB (584 albumin prime; 508 autologous blood prime) were evaluated for clinical outcomes in terms of mortality and length of hospitalization. In addition, over a period of 15 months, 1,458 patients in both the autologous blood/crystalloid group and the crystalloid only group were evaluated for the incidence of high-pressure excursions (HPE) after going on bypass. Comparative reviews of TP, COP and Plts demonstrated no significant difference 10 min after the start of bypass between Groups A and B. However, in Group C, there was a statistically significant increase in the intraoperative fluid requirements during CPB, compared to both of the other groups. There was no significant difference in the incidence of HPE, with an occurrence of 1.04% in the crystalloid only group and 1.11% in the autologous blood/crystalloid group. Autologous blood perfusates were identical to albumin perfusates in their platelet protection and reduction of fluid shifts during the intraoperative period.

The feedback response of Escherichia coli rRNA synthesis is not identical to the mechanism of growth rate-dependent control

Growth rate-independent rrn P1 promoter mutants were tested for their ability to respond to changes in rrn gene dosage. Most were found to be normal for the feedback response. In addition, cellular levels of the initiating nucleoside triphosphates remained unchanged when the rrn gene dosage was altered. These results suggest that the feedback response cannot be the mechanism for growth rate-dependent control of rRNA synthesis and that the relationship between these two processes may be more complicated than is currently understood.

Increased rrn gene dosage causes intermittent transcription of rRNA in Escherichia coli

When the number of rRNA (rrn) operons in an Escherichia coli cells is increased by adding an rrn operon on a multicopy plasmid, the rate of rRNA expression per operon is reduced to maintain a constant concentration of rRNA in the cell. We have used electron microscopy to examine rRNA transcription in cells containing a multicopy plasmid carrying rrnB. We found that there were fewer RNA polymerase molecules transcribing the rrn genes, as predicted from previous gene dosage studies. Furthermore, RNA polymerase molecules were arranged in irregularly spaced groups along the operon. No apparent pause or transcription termination sites that would account for the irregular spacing of the groups of polymerase molecules were observed. We also found that the overall transcription elongation rate was unchanged when the rrn gene dosage was increased. Our data suggest that when rrn gene dosage is increased, initiation events, or promoter-proximal elongation events, are interrupted at irregular time intervals.

Construction and initial characterization of Escherichia coli strains with few or no intact chromosomal rRNA operons

The Escherichia coli genome carries seven rRNA (rrn) operons, each containing three rRNA genes. The presence of multiple operons has been an obstacle to many studies of rRNA because the effect of mutations in one operon is diluted by the six remaining wild-type copies. To create a tool useful for manipulating rRNA, we sequentially inactivated from one to all seven of these operons with deletions spanning the 16S and 23S rRNA genes. In the final strain, carrying no intact rRNA operon on the chromosome, rRNA molecules were expressed from a multicopy plasmid containing a single rRNA operon (prrn). Characterization of these rrn deletion strains revealed that deletion of two operons was required to observe a reduction in the growth rate and rRNA/protein ratio. When the number of deletions was extended from three to six, the decrease in the growth rate was slightly more than the decrease in the rRNA/protein ratio, suggesting that ribosome efficiency was reduced. This reduction was most pronounced in the Delta7 prrn strain, in which the growth rate, unlike the rRNA/protein ratio, was not completely restored to wild-type levels by a cloned rRNA operon. The decreases in growth rate and rRNA/protein ratio were surprisingly moderate in the rrn deletion strains; the presence of even a single operon on the chromosome was able to produce as much as 56% of wild-type levels of rRNA. We discuss possible applications of these strains in rRNA studies.

An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria

Current global phylogenies are built predominantly on rRNA sequences. However, an experimental system for studying the evolution of rRNA is not readily available, mainly because the rRNA genes are highly repeated in most experimental organisms. We have constructed an Escherichia coli strain in which all seven chromosomal rRNA operons are inactivated by deletions spanning the 16S and 23S coding regions. A single E. coli rRNA operon carried by a multicopy plasmid supplies 16S and 23S rRNA to the cell. By using this strain we have succeeded in creating microorganisms that contain only a foreign rRNA operon derived from either Salmonella typhimurium or Proteus vulgaris, microorganisms that have diverged from E. coli about 120-350 million years ago. We also were able to replace the E. coli rRNA operon with an E. coli/yeast hybrid one in which the GTPase center of E. coli 23S rRNA had been substituted by the corresponding domain from Saccharomyces cerevisiae. These results suggest that, contrary to common belief, coevolution of rRNA with many other components in the translational machinery may not completely preclude the horizontal transfer of rRNA genes.

Control of rRNA transcription in Escherichia coli

The control of rRNA synthesis in response to both extra- and intracellular signals has been a subject of interest to microbial physiologists for nearly four decades, beginning with the observations that Salmonella typhimurium cells grown on rich medium are larger and contain more RNA than those grown on poor medium. This was followed shortly by the discovery of the stringent response in Escherichia coli, which has continued to be the organism of choice for the study of rRNA synthesis. In this review, we summarize four general areas of E. coli rRNA transcription control: stringent control, growth rate regulation, upstream activation, and anti-termination. We also cite similar mechanisms in other bacteria and eukaryotes. The separation of growth rate-dependent control of rRNA synthesis from stringent control continues to be a subject of controversy. One model holds that the nucleotide ppGpp is the key effector for both mechanisms, while another school holds that it is unlikely that ppGpp or any other single effector is solely responsible for growth rate-dependent control. Recent studies on activation of rRNA synthesis by cis-acting upstream sequences has led to the discovery of a new class of promoters that make contact with RNA polymerase at a third position, called the UP element, in addition to the well-known -10 and -35 regions. Lastly, clues as to the role of antitermination in rRNA operons have begun to appear. Transcription complexes modified at the antiterminator site appear to elongate faster and are resistant to the inhibitory effects of ppGpp during the stringent response.

rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation

Here we present evidence that only five of the seven rRNA operons present in Escherichia coli are necessary to support near-optimal growth on complex media. Seven rrn operons are necessary, however, for rapid adaptation to nutrient and temperature changes, suggesting it is the ability to adapt quickly to changing environmental conditions that has provided the selective pressure for the persistence of seven rrn operons in E. coli. We have also found that one consequence of rrn operon inactivation is a miscoordination of the concentrations of initiation factor IF3 and ribosomes.

Fracture of the internal lumen of a Datascope Percor Stat-DL Balloon, resulting in stroke

Intraaortic balloon counterpulsation was used to wean a 71-year-old man from cardiopulmonary bypass. Thirty-six hours after insertion, the internal lumen of the Datascope balloon fractured, releasing an unknown quantity of helium into the patient's circulation. Left-sided hemiparesis developed, secondary to a right hemispheric infarction.

Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies

The synthesis of ribosomal RNA is a complex and highly regulated process. To study this process, we have used deletion-insertions to disrupt sequentially from one to four of the seven rRNA (rrn) operons on the Escherichia coli genome. Inactivation of four rrn operons caused a 2.3-fold increase in the expression of a chloramphenicol acetyl transferase reporter gene fused to the tandem promoters of rrnA and a similar increase in the expression of the trp tRNA gene at the end of rrnC. This reflected enhanced expression of the remaining operons to compensate for having only three intact copies. The elevated expression was caused by an increase in both transcription initiation and RNA polymerase elongation rates specifically on rrn operons and occurred in the absence of changes in the intracellular concentration of ppGpp, suggesting that ppGpp is not involved in the regulation of this phenomenon. We discuss these results in relation to the ribosome feedback inhibition model described by Nomura and coworkers.

Comparison of the expression of the seven ribosomal RNA operons in Escherichia coli

We have compared the expression of the seven ribosomal RNA operons (rrn) of Escherichia coli and their responses to a variety of physiological and genetic perturbations. We used a set of rrn promoter fusion constructs in their native chromosomal positions to examine effects of chromosomal location on rrn operon expression and the same set of fusions on lambda lysogens to assay intrinsic promoter strengths independent of chromosome context. In its native chromosomal location, expression of the rrnH operon was significantly lower than expected. This effect was not attributable to weak promoter activity and was dependent on the growth medium. The rrnE operon had reduced promoter activity relative to the other ribosomal operons in minimal medium and thus appears to have abnormal growth rate regulation. The ribosomal RNA operons showed varied responses to amino acid starvation; expression of rrnD was inhibited most. There was only a slight increase in rrn transcription in response to a temperature shift (30 degrees C to 42 degrees C) and the differences between individual operons was very small. The rrnG operon showed a significantly lower response than the other ribosomal RNA operons to a depletion of the rrn transcription activator, Fis, and thus appears to have decreased Fis-mediated transactivation. Finally, the chromosomal fusion strains were used to study the effect on growth rate of inactivating each rrn operon. In fast growth conditions, loss of certain rrn operons caused subtle decreases in growth rate on complex medium.

ClpB is the Escherichia coli heat shock protein F84.1

ClpB is thought to be involved in proteolysis because of its sequence similarity to the ClpA subunit of the ClpA-ClpP protease. It has recently been shown that ClpP is a heat shock protein. Here we show that ClpB is the Escherichia coli heat shock protein F84.1. The F84.1 protein was overproduced in strains containing the clpB gene on a plasmid and was absent from two-dimensional gels from a clpB null mutation. Besides possessing a slower growth rate at 44 degrees C, the null mutant strain had a higher rate of death at 50 degrees C. We used reverse transcription of in vivo mRNA to show that the clpB gene was expressed from a sigma 32-specific promoter consensus sequence at both 37 and 42 degrees C. We noted that the clpB+ gene also caused the appearance of a second protein spot, F68.5, on two-dimensional gels. This spot was approximately 147 amino acids smaller than F84.1 and most probably is the result of a second translational start on the clpB mRNA. F68.5 can be observed on many published two-dimensional gels of heat-induced E. coli proteins, but the original catalog of 17 heat shock proteins did not include this spot.

Transcriptional termination sequence at the end of the Escherichia coli ribosomal RNA G operon: complex terminators and antitermination

We have examined the termination region sequence of the rrnG operon and have observed its properties in vivo using a fusion plasmid test system. Transcription of rrnG terminator fragments was also studied in vitro. We found that termination of rrnG transcription is a complex process controlled by a tandem Rho-independent and Rho-dependent terminator arrangement which we designate rrnG-tt'. Together, these two elements were 98% efficient at terminating transcription initiated at the rrnG-P2 promoter. When the two elements were separated, however, we found that the Rho-independent structure was only 59% efficient while the Rho-dependent fragment alone could account for total transcriptional termination of the tandem arrangement. The rrnG termination region was resistant to rrn antitermination and, therefore, possesses some means of stopping antiterminated transcription. The distal rrnG sequence contains several additional noteworthy features; the rrnGt' fragment contains a REP (repetitive extragenic palindromic) sequence and homology with a small unidentified reading frame following rrnE. This sequence is followed by witA, which is homologous to a citrate transport gene, citB. Finally, our sequence, obtained from plasmid pLC23-30, contains a Tn1000 insertion that is absent from the E. coli chromosome. This insertion lies 975 bp beyond the 5S gene and is not involved in the termination events examined in this study.

Antitermination of characterized transcriptional terminators by the Escherichia coli rrnG leader region

We have used a plasmid antitermination test system to examine the response of an Escherichia coli rRNA operon antiterminator to transcription through Rho-dependent and Rho-independent terminator-containing fragments. We also monitored transcription through multiple copies of a terminator to explore the mechanism of rrn antitermination. Four principal observations were made about antitermination and transcriptional terminators. (1) The rrn antiterminator mediated efficient transcription through Rho-dependent terminators. (2) Under the influence of the rrn antiterminator, RNA polymerase transcribed through two and three copies of the Rho-dependent 16 S----terminator with nearly the same efficiency as through one. (3) The antiterminator had less effect on fragments containing Rho-independent terminators; the rpoC t fragment and three fragments derived from the rrnB terminator region stopped antiterminated transcription. Four other Rho-independent terminator fragments were weakly antiterminated in our test system. (4) Surprisingly, the strength of these terminator fragments was not strongly related to properties such as the -delta G or number of trailing uridine residues of their canonical Rho-independent structures, but appears to be related to additional downstream terminators. We have drawn the following conclusions from these experiments. First, that ribosomal antitermination primarily reverses Rho-dependent termination by modifying the RNA polymerase elongation complex. Transcription through a 1700 nucleotide, multiple terminator sequence showed that the antiterminator caused persistent changes in the transcription process. Second, that fragments derived from the Rho-independent rrnB and rpoBC terminator regions can effectively stop antiterminated transcription. Third, that efficient in vivo termination may often involve regions with complex multiple terminators.

Conservation of the regulatory subunit for the Clp ATP-dependent protease in prokaryotes and eukaryotes

Bacteria, tomatoes, and trypanosomes all contain genes for a large protein with extensive homology to the regulatory subunit, ClpA, of the ATP-dependent protease of Escherichia coli, Clp. All members of the family have between 756 and 926 amino acids and contain two large regions, of 233 and 192 amino acids, each containing consensus sequences for nucleotide binding. Within these regions there is at least 85% similarity between the most distant members of the family. The high degree of similarity among the ClpA-like proteins suggests that Clp-like proteases are likely to be important participants in energy-dependent proteolysis in prokaryotic and eukaryotic cells.

Ribosomal RNA operon anti-termination. Function of leader and spacer region box B-box A sequences and their conservation in diverse micro-organisms

All Escherichia coli rrn operons show a common motif in which anti-terminator box B-box A sequences occur twice, first in the leader and again in the 16 S-23 S spacer. In this study we have analyzed several aspects of rrn anti-termination by leader and spacer anti-terminator sequences. Using DNA synthesis and a plasmid test system, we incorporated random changes into the leader anti-terminator region and examined these mutations for their ability to read through a strong terminator. We also examined anti-termination by synthetic box A and by rrn spacer region sequences. Information derived from these experiments was used to search the rrn sequences of other micro-organisms for possible anti-termination features. Our principal conclusions were that: (1) box A was sufficient for terminator readthrough; (2) we could show no positive requirement for box B in our test system; (3) many of the negative anti-terminator mutations caused a promoter up-effect in the absence of a terminator; (4) the search of rrn operons from other micro-organisms revealed that anti-terminator-like box B-box A sequences exist in leader and spacer regions of both eubacteria and archaebacteria. The frequent occurrence of this pattern suggested that the E. coli rrn anti-termination motif is widespread in nature and has been conserved in microbial evolution.

Loss of the spacer loop sequence from the rrnB operon in the Escherichia coli K-12 subline that bears the relA1 mutation

A polymorphism affecting the spacer region of the rrnB rRNA operon is described. Strains from a major Escherichia coli K-12 subbranch are missing a 106-nucleotide portion of the rrnB 16S-to-23S spacer, and a 20-nucleotide sequence is found in its place. We have called this mutant operon rrnB2. The rrnB2 spacer was most probably derived from either rrnC or rrnE. This alteration of rrnB may have occurred by a recombinational exchange or by gene conversion. In the genealogy of E. coli K-12 strains, the appearance of rrnB2 is associated with the spontaneous occurrence of the first relaxed mutation, but attempts to show a selective relationship between the two mutational events have had negative results. The sequences of the rrnG and rrnC 16S-to-23S spacers have also been determined and their comparisons to the other rrn operons encoding tRNAGlu2 are presented.

In vivo translation of a region within the rrnB 16S rRNA gene of Escherichia coli

In this study we show that a segment of the Escherichia coli rrnB 16S gene can be translated in vivo. Other laboratories have previously reported that there are internal transcription and translation signals and open reading frames within the E. coli rrnB rRNA operon. Their studies revealed a translation start signal followed by a 252-base-pair open reading frame (ORF16) within the 16S gene and detected a promoter (p16) in the same general region by using in vitro RNA polymerase binding and transcription initiation assays. By using plasmid gene fusions of ORF16 to lacZ we showed that an ORF16'-'beta-galactosidase fusion protein was made in vivo. Transcripts encoding the fusion protein were expressed either from the rrnB p1p2 control region or from a hybrid trp-lac promoter (tacP), but the amount of expression was considerably less than for a lacZ control plasmid. We used fusions to the cat gene to show that p16 is one-half as active as lacP. Deletions were used to show that p16 is located within ORF16 and thus cannot promote a transcript encoding the ORF16 peptide. A comparison of sequences from different organisms shows that ORF16 and p16 lie in a highly conserved region of the procaryotic 16S RNA structure. The first 20 amino acids of ORF16 are conserved in most eubacterial and plant organellar sequences, and promoter activity has been detected in this region of the Caulobacter crescentus sequence by other workers.

Antitermination of E. coli rRNA transcription is caused by a control region segment containing lambda nut-like sequences

We have localized the antitermination system involved in E. coli ribosomal RNA transcription and compared it with antitermination in the lamboid bacteriophages. In vivo experiments with gene-fusion plasmids were used to examine the ability of specific areas of the rrnG control region to convert an ordinary transcription complex into antitermination transcription complex. A 67 bp restriction fragment immediately following the rrnG P2 promoter decreased transcription termination about 50%. This fragment contains box A-, box B-, and box C-like sequences similar to those in lambda nut loci. It also caused transcripts from lac and hybrid trp-lac promoters to read through a transcription terminator. Translation through the 67 bp segment or reversal of its orientation resulted in complete loss of antitermination activity. We conclude that the E. coli ribosomal RNA operons possess an antitermination system similar to that used by the bacteriophage lambda.

Evidence for antitermination in Escherichia coli RRNA transcription

The stable RNA operons of Escherichia coli do not exhibit polarity, even though they make an RNA product that is not translated. By contrast, most E. coli operons that specify proteins exhibit polarity if their translation is interrupted. The transcriptional component of this polarity depends on the action of Rho protein on the exposed mRNA, which results in premature transcription termination. Here we examine how a stable RNA operon (rrnG) transcript is protected from the Rho protein-mediated polarity response. We compared transcription from the ara and the rrnG promoters through a 16S DNA segment. In each case, the promoter-16S sequences were joined to a trp-lac fusion, and lacZ mRNA was examined in rho+ and rho-115 strains. We found significant Rho protein-dependent termination of transcripts from the ara promoter but little or no Rho protein effect on transcription from the rrnG promoter. We concluded that the transcript of the 16S ribosomal DNA segment does contain Rho protein-dependent transcription terminators, but there is an antitermination system in the rrnG control region that allows it to transcribe through those terminators.

Translational coupling of the trpB and trpA genes in the Escherichia coli tryptophan operon

We investigated whether there is translational coupling between the tryptophan operon trpB and trpA genes in Escherichia coli. A trp-lac fusion system was used in which part of the trpA gene is fused to the lacZ gene. This fusion protein has the translation initiation site of trpA but retains beta-galactosidase activity. We introduced a frameshift mutation early in trpB and measured its effect on transcription and translation of the trp-lac fusion. The mutation resulted in a 10-fold drop in beta-galactosidase activity but only a 2-fold drop in lacZ mRNA or galactoside transacetylase levels. An rho mutation restored the lacZ mRNA and transacetylase levels to those of the control but only increased the beta-galactosidase level to 20% that of the control. We conclude from these results that if the trpB gene is not translated, efficient translation of the trpA'-lac'Z mRNA does not occur and, thus, that these genes are translationally coupled. The implication of this finding for other studies with gene fusions is discussed.

The regulatory region of the divergent argECBH operon in Escherichia coli K-12

The nucleotide sequence of the control region of the divergent argECBH operon has been established in the wild type and in mutants affecting expression of these genes. The argE and argCBH promoters face each other and overlap with an operator region containing two domains which may act as distinct repressor binding sites. A long leader sequence - not involved in attenuation - precedes argCBH. Overlapping of the argCBH promoter and the region involved in ribosome mobilization for argE translation explains the dual effect of some mutations. Mutations causing semi-constitutive expression of argE improve putative promoter sequences within argC. Implications of these results regarding control mechanisms in amino acid biosynthesis and their evolution are discussed.

Nucleotide sequence of the rrnG ribosomal RNA promoter region of Escherichia coli

The primary structure of the promoter region for a ribosomal RNA transcription unit (rrnG) of Escherichia coli K12 has been determined. The sequence was obtained from 1 1.5 kbp EcoRI fragment derived from the hybrid plasmid pLC23-30. This fragment contains 455 bp preceding P1 of the rrnG promoter region and 674 bp of the rrnG 16S RNA gene. The sequence before the rrnG promoter region contains an open reading frame (ORF-BG) followed by a possible hairpin structure that resembles other known transcription terminators. The sequence of the rrnG promoter region is similar but not identical to that of rrnA and rrnB. Several minor differences between the sequences of the 16S RNA genes of rrnG and rrnB were also noted. In addition, sequences were found that could generate special structures involving the promoter regions of rrn loci. Such structures are described and their possible involvement in the regulation of ribosomal RNA synthesis is discussed.

Nucleotide sequence at the end of the gene for the RNA polymerase beta' subunit (rpoC)

We have determined the DNA sequence surrounding the transcription terminator following rpoC, the gene that codes for the beta' subunit of RNA polymerase in E. coli K12. The 2044 bp sequence obtained contains the distal 335 codons of rpoC followed by a 212 bp non-coding region and a second open reading frame (ORFa) of 179 codons. The final 181 nucleotides of the sequence form the 5' end of a third open reading frame (ORFb). The in vivo 3' end of the rpoC mRNA was located by analysis of RNA/DNA hybrids cleaved with nuclease S1 (S1 mapping). These results indicated that the major transcription termination of the rplJL-rpoBC transcription unit occurs a short distance past the translation stop codon for rpoC. Four regions of symmetry, suggesting secondary structure in the mRNA, were found in the DNA sequence near the rpoC translation termination codon. The last of these hairpin structures is similar to other rho-independent transcription terminators and its 3' end coincides with the end of the rpoC mRNA as predicted by S1-mapping. Inspection of the open reading frames indicates that rpoC uses a high percentage of codons that are recognized by the major tRNA species of E. coli while ORFa and ORFb contain many codons recognized by minor tRNA species. ORFa specifies a very basic peptide.

Attenuation and processing of RNA from the rplJL--rpoBC transcription unit of Escherichia coli

Attenuation and processing of the mRNA from the ribosomal protein-RNA polymerase operon rplJL--rpoBC have been demonstrated by the analysis of nuclease SI-resistant RNA . DNA hybrids. These hybrids were formed between RNA produced in vivo and specific DNA restriction fragments which span the rplL--rpoB intercistronic region. The 3' end of the predominant attenuated RNA lies 69 nucleotides beyond the end of the rplL gene following sequence features that are similar to those of other known attenuators. The nonattenuated transcript is normally cleaved in the intercistronic region. However, in an RNase III mutant strain, the hybrids corresponding to the cleaved nonattenuated mRNAs disappear and the expected full-sized hybrid is seen. We have localized the cleavage to an area of possible secondary structure in the transcript approximately 200 nucleotides beyond the end of the rplL gene. This demontrates RNase III processing of Escherichia coli mRNA. The methods used in this study permit the examination of specific ends of large and complex polycistronic mRNAs. Such experiments should help in understanding how posttranscriptional events influence gene expression.

Control features within the rplJL-rpoBC transcription unit of Escherichia coli

Gene fusions constructed in vitro have been used to examine transcription regulatory signals from the operon which encodes ribosomal proteins L10 and L7/12 and the RNA polymerase beta and beta' subunits (the rplJL-rpoBC operon). Portions of this operon, which were obtained by in vitro deletions, have been placed between the ara promoter and the lacZ gene in the gene-fusion plasmid pMC81 developed by M. Casadaban and S. Cohen. The effect of the inserted DNA segment on the expression of the lacZ gene (in the presence and absence of arabinose) permits the localization of regulatory signals to discrete regions of the rplJL-rpoBC operon. An element that reduces the level of distal gene expression to one-sixth is located on a fragment which spans the rplL-rpoB intercistronic region. This strongly supports the idea that there is an attenuator in this region. The terminator for the operon is located on a fragment which spans the 3' end of the rpoC gene. The major promoter for the operon precedes the rplJ gene [Yamamoto, M. & Nomura, M. (1978) Proc. Natl. Acad. Sci. USA 75, 3891-3895 and Linn, T. & Scaife, J. (1978) Nature (London) 276, 33-37] and was not examined in this study. However, a weak promoter is observed on the fragment that spans the rplJ-rplL intercistronic region. Other regions of the operon may also contain weak promoters. The contribution of these elements to the regulation of this complex operon is discussed.

Growth inhibition of Escherichia coli K-12 by L-valine: a consequence of a regulatory pattern

We studied the production of the ilvG gene product, the valine resistant acetolactate synthase isoenzyme II, in an ilvO+ G+ ilvB ilvHI derivative of Escherichia coli K-12. This strain contains mutations in the structural genes for the valine sensitive acetolactate synthase isoenzymes I and III. We find that the ilvG gene is not expressed in this strain when gworn with either isoleucine and valine or with isoleucine, leucine and valine, or when limited for either isoleucine or valine. Since we previously found that the ilvG gene is expressed in an ilvO603 containing strain (Favre et al., 1976), we presume that the mechanism by which E. coli K-12 regulates the ilv gene cluster is responsible for the lack of ilvG expression in the ilvO+ strain. The valine sensitivity of E. Coli K-12 is a consequence of this regulatory pattern.

Nucleotide sequence of region preceding trp mRNA initiation site and its role in promoter and operator function

The nucleotide sequence of the region preceding the transcription initiation site of the tryptophan operon of Escherichia coli was determined. Essentially all of the trp operator precedes the transcribed portion of the operon. The deduced sequence contains the recognition site of endonuclease Hpa I. This site is protected from Hpa I cleavage by RNA polymerase and by trp repressor. Regions of 2-fold symmetry are present in the DNA sequence.

The gastrointestinal absorption of methadone in the rat

The absorption of dl-methadone from the gastrointestinal tract of the Sprague-Dawley rat was examined by the in vivo segment technique. Duodenal absorption, measured as a function of time and dose, followed first-order kinetics with a half-life of 15.6 min. Absorption was not influenced by prior or concomitant administration of a variety of drugs. Absorption from other regions of the intestine was similar to that from the duodenum; in contrast, absorption from the stomach was markedly slower. Gastric absorption was increased by alkalinization of stomach contents but was still considerably slower than from the duodenum. Gastric emptying of methadone appears to be the rate-limiting step in the overall gastrointestinal absorption of the drug, since the rate of emptying following intubation of the drug into the stomach was also considerably slower than the rate of duodenal absorption.