Movement of the decoding region of the 16 S ribosomal RNA accompanies tRNA translocation

The ribosome undergoes pronounced periodic conformational changes during protein synthesis. Of particular importance are those occurring around the decoding site, the region of the 16 S rRNA interacting with the mRNA-(tRNA)(2) complex. We have incorporated structural information from X-ray crystallography and nuclear magnetic resonance into cryo-electron microscopic maps of ribosomal complexes designed to capture structural changes at the translocation step of the polypeptide elongation cycle. The A-site region of the decoding site actively participates in the translocation of the tRNA from the A to the P-site upon GTP hydrolysis by elongation factor G, shifting approximately 8 A toward the P-site. This implies that elongation factor G actively pushes both the decoding site and the mRNA/tRNA complex during translocation.

A single amino acid residue on the alpha(5) subunit (Ile215) is essential for ligand selectivity at alpha(5)beta(3)gamma(2) gamma-aminobutyric acid(A) receptors

Imidazobenzodiazepines such as RY-80 have been reported to exhibit both high affinity and selectivity for GABA(A) receptors containing an alpha(5) subunit. A single amino acid residue (alpha(5)Ile215) has been identified that plays a critical role in the high-affinity, subtype-selective effects of RY-80 and structurally related ligands. Thus, substitution of alpha(5)Ile215 with the cognate amino acid contained in the alpha(1) subunit (Val211) reduced the selectivity of RY-80 for alpha(5)beta(3)gamma(2) receptors from approximately 135- to approximately 8-fold compared with alpha(1)beta(3)gamma(2) receptors. This mutation produced a comparable reduction in the selectivity of RY-24 (a structural analog of RY-80) for alpha(5)beta(3)gamma(2) receptors but did not markedly alter the affinities of ligands (e.g., flunitrazepam) that are not subtype-selective. Conversely, substitution of the alpha(1) subunit with the cognate amino acid contained in the alpha(5) subunit (i.e., alpha(1)V211I) increased the affinities of alpha(5)-selective ligands by a approximately 20-fold and reduced by 3-fold the affinity of an alpha(1)-selective agonist (zolpidem). Increasing the lipophilicity (e.g., by substitution of Phe) of alpha(5)215 did not significantly affect the affinities (and selectivities) of RY-80 and RY-24 for alpha(5)-containing GABA(A) receptors. However, the effect of introducing hydrophilic and or charged residues (e.g., Lys, Asp, Thr) at this position was no greater than that produced by the alpha(5)I215V mutation. These data indicate that residue alpha(5)215 may not participate in formation of the lipophilic L(2) pocket that has been proposed to contribute to the unique pharmacological properties of alpha(5)-containing GABA(A) receptors. RY-80 and RY-24 acted as inverse agonists in both wild-type alpha(5)beta(3)gamma(2) and mutant alpha(5)I215Kbeta(3)gamma(2) receptors expressed in Xenopus laevis oocytes. However, both RY-24 and RY-80 acted as antagonists at mutant alpha(5)I215Vbeta(3)gamma(2) and alpha(5)I215Tbeta(3)gamma(2) receptors, whereas the efficacy of flunitrazepam was similar at all three receptor isoforms. The data demonstrate that amino acid residue alpha(5)215 is a determinant of both ligand affinity and efficacy at GABA(A) receptors containing an alpha(5) subunit.

The control of morph development in the parasitic nematode Strongyloides ratti

The parasitic nematode Strongyloides ratti has a complex life cycle. The progeny of the parasitic females can develop into three distinct morphs, namely directly developing infective third-stage larvae (iL3s), free-living adult males and free-living adult females. We have analysed of the effect of host immune status (an intra-host factor), environmental temperature (an extra-host factor) and their interaction on the proportion of larvae that develop into these three morphs. The results are consistent with the developmental decision of larvae being controlled by at least two discrete developmental switches. One is a sex-determination event that is affected by host immune status and the other is a switch between alternative female morphs that is affected by both host immune status and environmental temperature. These findings clarify the basis of the life cycle of S. ratti and demonstrate how such complex life cycles can result from a combination of simple developmental switches.

Molecular belt models for the apolipoprotein A-I Paris and Milano mutations

Models for the binding of the 200-residue carboxy-terminal domain of two mutants of apolipoprotein A-I (apo A-I), apo A-I(R173C)(Milano) and apo A-I(R151C)(Paris), to lipid in discoidal high-density lipoprotein (HDL) particles are presented. In both models, two monomers of the mutant apo A-I molecule bind to lipid in an antiparallel manner, with the long axes of their helical repeats running perpendicular to the normal of the lipid bilayer to form a single disulfide-linked homodimer. The overall structures of the models of these two mutants are very similar, differing only in helix-helix registration. Thus these models are consistent with experimental observations that reconstituted HDL particles containing apo A-I(Milano) and apo A-I(Paris) are very similar in diameter to reconstituted HDL particles containing wild-type apo A-I, and they support the belief that apo A-I binds to lipid in discoidal HDL particles via the belt conformation.

Detailed molecular model of apolipoprotein A-I on the surface of high-density lipoproteins and its functional implications

The major apolipoprotein (apo) A-I containing lipoprotein, high- density lipoprotein, is a negative risk factor for cardiovascular disease. An atomic resolution molecular model for lipid-associated apo A-I was recently proposed in which two apo A-I molecules are wrapped beltwise around a small discoidal patch of phospholipid bilayer. Because of its detailed predictions of lipid-associated apo A-I structure, this molecular belt model, if confirmed, provides a blueprint for understanding the molecular mechanisms of reverse cholesterol transport, and thus for the rational design of new classes of drugs for reversal of atherosclerosis and cardiovascular disease. The details and implications of the model are currently being explored by site-directed mutagenesis.

Structure and function of apolipoprotein A-I and high-density lipoprotein

Structural biology and molecular modeling have provided intriguing insights into the atomic details of the lipid-associated structure of the major protein component of HDL, apo A-I. For the first time, an atomic resolution map is available for future studies of the molecular interactions of HDL in such biological processes as ABC1-regulated HDL assembly, LCAT activation, receptor binding, reverse lipid transport and HDL heterogeneity. Within the context of this paradigm, the current review summarizes the state of HDL research.

The antibacterial and NMDA receptor activating properties of aminoglycosides are dissociable

The use of aminoglycoside antibiotics is limited by side effects, the most critical of which are vestibular and cochlear toxicity. Recent evidence indicates that these effects result from an excitotoxic process mediated, at least in part, through a polyamine-like activation of NMDA receptors. This study investigated whether these positive modulatory effects of aminoglycosides at NMDA receptors are dissociable from their antibacterial properties. A group of structurally related apramycin derivatives was evaluated for the ability to enhance [3H]dizocilpine binding to rat brain membranes, and for the ability to augment agonist responses on recombinant (NR1A/2B) NMDA receptors expressed in Xenopus oocytes. Based on the antibacterial potencies of these derivatives against Staphylococcus aureus and Escherichia coli, it is concluded that there is no correlation between the ability of an aminoglycoside to produce a positive modulation of NMDA receptors and minimum inhibitory antibacterial concentrations. These findings indicate that it may be possible to develop an aminoglycoside antibiotic with reduced potential for ototoxicity.

A detailed molecular belt model for apolipoprotein A-I in discoidal high density lipoprotein

Apolipoprotein A-I (apoA-I) is the principal protein of high density lipoprotein particles (HDL). ApoA-I contains a globular N-terminal domain (residues 1-43) and a lipid-binding C-terminal domain (residues 44-243). Here we propose a detailed model for the smallest discoidal HDL, consisting of two apoA-I molecules wrapped beltwise around a small patch of bilayer containing 160 lipid molecules. The C-terminal domain of each monomer is ringlike, a curved, planar amphipathic alpha helix with an average of 3.67 residues per turn, and with the hydrophobic surface curved toward the lipids. We have explored all possible geometries for forming the dimer of stacked rings, subject to the hypothesis that the optimal geometry will maximize intermolecular salt bridge interactions. The resulting model is an antiparallel arrangement with an alignment matching that of the (nonplanar) crystal structure of lipid-free apoA-I.

Stability of meperidine in an implantable infusion pump using capillary gas chromatography-mass spectrometry and a deuterated internal standard

A capillary gas chromatographic-mass spectrometric (GC MS) method is described for the analysis of meperidine using 3,3,5,5-[2H4]-meperidine as an internal standard. Chromatography was performed on a (5% phenyl) methylpolysiloxane column (30 m x 0.32 mm I.D., 0.25 microm film thickness) operated at 195 degrees C; helium carrier gas-50 cm/s(-1), tR = 2.3 min. Ionization was by electron impact (EI) and detection by selected ion monitoring of the molecular ions. The method provided high response linearity (mean r = 0.9982) and precision (< 6.5% C.V.). Application of this method to a pilot study of aqueous meperidine x HCl (10 mg/ml(-1)) stability in a surgically implantable infusion pump at 37 degrees C for 90 days revealed no demonstrable drug degradation.

Polyamine-like actions of aminoglycosides at recombinant N-methyl-D-aspartate receptors

Recent pharmacological studies have led to the hypothesis that aminoglycoside-induced ototoxicity is an excitotoxic process mediated, at least in part, by a polyamine-like modulation of N-methyl-D-aspartate (NMDA) receptors. To explore this hypothesis, we compared the effects of several aminoglycosides (neomycin B, kanamycin A, streptomycin, and dihydrostreptomycin) with spermine on recombinant NMDA receptors of defined composition expressed in Xenopus oocytes. Like spermine, aminoglycosides potentiate agonist-induced responses in the presence of both saturating glycine ("glycine-independent") and subsaturating glycine ("glycine-dependent") concentrations on NR1A/2B receptors. Likewise, aminoglycosides and spermine potentiated the agonist responses under glycine-dependent conditions on NR1A/2A receptors. Despite these similarities, several prominent differences were observed between spermine and aminoglycosides as well as among individual aminoglycosides. For example, neomycin B, streptomycin, and kanamycin A, but neither spermine nor dihydrostreptomycin, potentiated glycine-dependent responses on NR1A/2C receptors. Differences between spermine and aminoglycosides also were observed with respect to the voltage dependence of polyamine-like actions. For example, under glycine-dependent conditions, potentiation at NR1A/2B receptors by spermine was voltage dependent, decreasing as the holding potential was changed from -35 to -85 mV; in contrast, potentiation induced by aminoglycosides at NR1A/2B receptors was voltage independent. No direct relationships emerged between the effect of an aminoglycoside at a specific NMDA receptor subtype and the ototoxicity of these antibiotics.

Heterogeneity in the distribution of Strongyloides ratti infective stages among the faecal pellets of rats

The distribution of helminth parasites within their host population is usually overdispersed and can be described by the negative binomial distribution. The causes of this overdispersion are poorly understood, but heterogeneity in the distribution of infective stages within the environment has been implicated as a possible factor. Here we describe the distribution of infective stages of the rat intestinal nematode parasite Strongyloides ratti among the faecal pellets of its host. The distribution of infective stages between faecal pellets is overdispersed and well described by the negative binomial distribution. This overdispersion increases during the course of infection and occurs over a range of infection intensities. Overdispersion of nematode infective stages among faecal pellets may result in increased spatial heterogeneity of the infective stages in the environment and thus may contribute to the generation of overdispersion of adult parasitic stages. In addition, these findings raise important issues regarding the accurate quantification of helminth egg counts from faecal samples.

Image-guided core breast biopsy of ductal carcinoma in situ presenting as a non-calcified abnormality

OBJECTIVE

Ductal carcinoma in situ (DCIS) typically presents as calcifications which are detected mammographically. Our aim was to evaluate the less common presentations of ductal carcinoma in situ diagnosed by image-guided core biopsy and correlate with histopathologic diagnoses.

METHODS AND MATERIAL

Imaging and histopathologic findings were retrospectively reviewed in 11 patients with ductal carcinoma in situ diagnosed at core biopsy that presented as noncalcified radiographic abnormalities.

RESULTS

Mammography showed non-calcified, circumscribed nodules, ill-defined nodules and architectural distortion. In two patients, no mammographic abnormality was detected. Sonography showed circumscribed, round or oval, solid masses; irregular, heterogeneous masses; and a tubular structure. Histopathologic diagnoses included multiple architectural subtypes and ranged from low to high nuclear grade.

CONCLUSION

Although image-guided core biopsy diagnosis of ductal carcinoma is typically made when sampling calcifications, DCIS can be diagnosed following biopsy of non-calcified masses or distortion. There is no correlation between histopathologic subtype and radiologic appearance.

Large-core needle biopsy of nonpalpable breast lesions

CONTEXT

An increasing number of nonpalpable abnormalities requiring breast biopsy are being identified due to the widespread use of screening mammography. Large-core needle biopsy (LCNB) has become an alternative to surgical excision.

OBJECTIVE

To determine whether LCNB is a safe and accurate technique to evaluate nonpalpable abnormalities found on breast imaging studies.

DESIGN AND SETTING

Case series at an institutional referral center from August 1, 1991, to December 31, 1997.

PATIENTS

A total of 1643 women with 1 or more suspicious breast abnormalities received LCNBs (n = 1836 lesions).

INTERVENTION

The LCNB of the breast uses a 14- or 11-gauge needle with stereotactic localization or ultrasound guidance.

MAIN OUTCOME MEASURE

Utility and potential limitations of LCNB compared with the criterion standard, surgical excision after wire localization.

RESULTS

Of the 1836 breast lesions sampled, 444 (24%) were found to be malignant. A total of 412 (22%) were found to be malignant on the initial LCNB and 202 repeat biopsies yielded 32 additional malignancies. Complications were infrequent: 1 patient experienced a superficial infection and 1 developed a pneumothorax after LCNB.

CONCLUSION

Image-guided LCNB is a reliable diagnostic alternative to surgical excision of suspicious nonpalpable breast abnormalities.

Fibrous nodules found at large-core needle biopsy of the breast: imaging features

PURPOSE

To describe the imaging and histologic features of large-core needle biopsy (LCNB) specimens of fibrous nodules.

MATERIALS AND METHODS

Of 853 breast masses in which LCNB was performed, 38 (4%) revealed histologic findings of fibrous nodules. Repeat biopsy was performed in 16 lesions (surgical excision, 13 lesions; repeat LCNB, three lesions). The mammographic and ultrasonographic findings in these 16 cases, the histologic LCNB findings, and the repeat biopsy findings were retrospectively reviewed.

RESULTS

Repeat biopsy findings confirmed the diagnosis of fibrous nodules in 15 of the 16 masses. In one mass, repeat LCNB findings showed a fibroadenoma. The imaging features of the fibrous nodules varied. Five nodules (33%) manifested as masses with indistinct margins; six (40%), as circumscribed masses. In four cases (27%), imaging suggested malignancy. None were calcified masses. An additional 22 masses had circumscribed or indistinct borders and were diagnosed with LCNB as fibrous nodules. None of these masses had suspicious findings, and repeat biopsy was not performed.

CONCLUSION

Fibrous nodules usually manifest as masses with circumscribed or indistinct margins but can have findings suggestive of malignancy. LCNB can reveal histologic findings consistent with this diagnosis. In all masses in which repeat biopsy was performed, the diagnosis of a fibrous nodule was confirmed or another benign stromal lesion was diagnosed.

Molecular dynamics on a model for nascent high-density lipoprotein: role of salt bridges

The results of an all-atom molecular dynamics simulation on a discoidal complex made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and a synthetic alpha-helical 18-mer peptide with an apolipoprotein-like charge distribution are presented. The system consists of 12 acetyl-18A-amide (Ac-18A-NH2) (. J. Biol. Chem. 260:10248-10255) molecules and 20 molecules of POPC in a bilayer, 10 in each leaflet, solvated in a sphere of water for a total of 28,522 atoms. The peptide molecules are oriented with their long axes normal to the bilayer (the "picket fence" orientation). This system is analogous to complexes formed in nascent high-density lipoprotein and to Ac-18A-NH2/phospholipid complexes observed experimentally. The simulation extended over 700 ps, with the last 493 ps used for analysis. The symmetry of this system allows for averaging over different helices to improve sampling, while maintaining explicit all-atom representation of all peptides. The complex is stable on the simulated time scale. Several possible salt bridges between and within helices were studied. A few salt bridge formations and disruptions were observed. Salt bridges provide specificity in interhelical interactions.

Three-dimensional placement of the conserved 530 loop of 16 S rRNA and of its neighboring components in the 30 S subunit

Nucleotides 518-533 form a loop in ribosomal 30 S subunits that is almost universally conserved. Both biochemical and genetic evidence clearly implicate the 530 loop in ribosomal function, with respect both to the accuracy control mechanism and to tRNA binding. Here, building on earlier work, we identify proteins and nucleotides (or limited sequences) site-specifically photolabeled by radioactive photolabile oligoDNA probes targeted toward the 530 loop of 30 S subunits. The probes we employ are complementary to 16 S rRNA nucleotides 517-527, and have aryl azides attached to nucleotides complementary to nucleotides 518, 522, and 525-527, positioning the photogenerated nitrene a maximum of 19-26 A from the complemented rRNA base. The crosslinks obtained are used as constraints to revise an earlier model of 30 S structure, using the YAMMP molecular modeling package, and to place the 530 loop region within that structure.

Major groove binding of the tRNA/mRNA complex to the 16 S ribosomal RNA decoding site

We propose a detailed three-dimensional model, with atomic detail, for the structure of the Escherichia coli 16 S rRNA decoding site in a complex with mRNA and the A and P-site tRNAs. Model building began with four primary assumptions: (1) A and P-site tRNA conformations are identical with those seen in the tRNA crystal structure; (2) A and P-site tRNAs adopt an S-type orientation upon binding mRNA in the ribosome; (3) A1492 and A1493 bind non-specifically to the mRNA through a series of hydrogen bonds; and (4) C1400 lies in close proximity to the P-site tRNA wobble base in order to satisfy a UV-induced photocrosslink formed between the two residues. We have models with both major groove and minor groove binding of the tRNA/mRNA complex to the decoding site RNA, and conclude that major groove binding is more likely. Both classes of models maintain structural features reported in the NMR structure of the A-site region of the decoding site RNA with bound paromomycin. We also present models for the tRNA/mRNA complex bound to the decoding site RNA in the presence of the aminoglycoside paromomycin. We discuss possible mechanisms for ribosomal proof reading and antibiotic disruption of this proofreading.

Individualized outcome feedback produces voluntary antiemetic prescribing practice changes

STUDY OBJECTIVE

To determine the impact of individualized outcome feedback on antiemetic prescribing practices and compare outcomes of a cost-effective, standardized antiemetic protocol (PROT) to that of customized antiemetic therapy (NONPROT).

DESIGN

Prospective, observational study with randomized component.

SETTING

Postanesthesia care unit (PACU) of an academic medical center.

PATIENTS

3027 consecutive ASA physical status I, II, and III patients receiving general anesthesia.

INTERVENTIONS

Patients were randomized to receive 0.625 mg droperidol or 4 mg ondansetron for postoperative nausea and/or vomiting (PONV) from a protocol, or received customized antiemetic therapy.

MEASUREMENTS AND MAIN RESULTS

Incidence of PACU PONV, selection of PROT versus NONPROT, patient satisfaction, and use of PONV prophylaxis were measured and indexed by an attending anesthesiologist in a monthly report for 4 months. Monthly expenditures for antiemetic therapy prior to, during, and after the study were collected. Literature on PONV outcomes, appropriate timing, and selection of PONV prophylaxis was distributed. The NONPROT group was slightly older than the PROT group; otherwise, demographics were similar between all groups. The incidence of PONV did not differ between the PROT and NONPROT groups (11% vs. 10%), and the incidence of PONV in patients receiving prophylaxis was higher in both groups (17% PROT vs. 15% NONPROT). Patients receiving ondansetron as a first-line drug required rescue therapy less often (5%) than those receiving droperidol (14%); however, patient satisfaction was indistinguishable among all groups. During the study, the use of prophylaxis decreased 47% without an increase in PONV, and PROT selection increased 54%.

CONCLUSIONS

Individualized outcome feedback produced a 48% reduction in monthly expenditures for ondansetron and droperidol, which was sustained after the study. Patients satisfaction between ondansetron 4 mg and droperidol 0.625 mg given in the PACU did not differ in spite of a slightly greater efficacy of ondansetron as a first-line drug.

Exploring three-dimensional structures of the HIV-1 RNA/tRNALys3 initiation complex

Human immunodeficiency virus type 1 (HIV-1) uses host tRNA as a primer for reverse transcription of its viral RNA. The 3' terminal 18 nucleotides of human tRNALys3 are complementary to the primer binding site on the viral RNA. A secondary structure model for the HIV-1 RNA/tRNALys3 initiation complex has been proposed that includes additional base-pairing between the tRNA and the HIV-1 RNA beyond the 18 nucleotides of the primer binding site. Included in these interactions is base-pairing between the anticodon of tRNALys3 and an A-rich loop in the HIV-1 secondary structure. The tRNA and HIV-1 RNA are significantly unfolded from their native structures in order to form the initiation complex proposed in this model. We have found several problems with the proposed secondary structure in our efforts to build a three-dimensional model that is compatible with it. The additional interactions between the tRNA and viral RNA cause the structure to be topologically knotted. This poses a problem for folding of the initiation complex and transcription by reverse transcriptase. We have also not been able to build any all-atom models based on known RNA structures that follow the secondary structure model in the extended tRNA/HIV-1 RNA complex. Finally, beyond the primer binding site interaction, subsequent biochemical and genetic studies have given further insight into the structure of the initiation complex. These results call into question some of the extended HIV-1 RNA/tRNA interactions that have been proposed.

To knot or not to knot? Examination of 16S ribosomal RNA models

The presence of topological knots in large RNA structures is highly unlikely given that 1) no RNA structures determined thus far contain topological knots, 2) secondary structure maps for most RNA molecules are knot free, 3) there are no known RNA topoisomerases, and 4) it is difficult to imagine how knots could be formed specifically and uniquely during transcription. Since native RNA structures probably lack topological knots, models of these RNA molecules should be free of knots as well. Therefore, we have examined four existing models for the 30S ribosomal subunit to determine if any of the three domains of the 16S rRNA molecule is knotted. We found that all but one model had at least one knotted domain. We conclude that models of large RNA molecules should be examined for knotting before publication.

Continuous spinal anesthesia for cesarean section in a parturient with severe preeclampsia

Epidural anesthesia is a widely accepted technique for cesarean section in the preeclamptic patient with normal coagulation. Regional anesthetic techniques avoid the hazards associated with tracheal intubation in the preeclamptic or eclamptic patient. To date, continuous spinal anesthesia in the preeclamptic parturient has not been described. We present a case in which continuous spinal anesthesia was administered for cesarean section in a morbidly obese parturient with severe preeclampsia. Continuous spinal anesthesia was successfully administered without significant hemodynamic consequences or maternal or fetal morbidity. This case suggests that continuous spinal anesthesia may be a viable alternative anesthetic technique for operative delivery in the preeclamptic parturient when epidural anesthesia cannot be established.