A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome

BACKGROUND

This study addresses the general problem of dividing a density map of a nucleic-acid-protein complex obtained by cryo-electron microscopy (cryo-EM) or X-ray crystallography into its two components. When the resolution of the density map approaches approximately 3 A it is generally possible to interpret its shape (i. e., the envelope obtained for a standard choice of threshold) in terms of molecular structure, and assign protein and nucleic acid elements on the basis of their known sequences. The interpretation of low-resolution maps in terms of proteins and nucleic acid elements of known structure is of increasing importance in the study of large macromolecular complexes, but such analyses are difficult.

RESULTS

Here we show that it is possible to separate proteins from nucleic acids in a cryo-EM density map, even at 11.5 A resolution. This is achieved by analysing the (continuous-valued) densities using the difference in scattering density between protein and nucleic acids, the contiguity constraints that the image of any nucleic acid molecule must obey, and the knowledge of the molecular volumes of all proteins.

CONCLUSIONS

The new method, when applied to an 11.5 A cryo-EM map of the Escherichia coli 70S ribosome, reproduces boundary assignments between rRNA and proteins made from higher-resolution X-ray maps of the ribosomal subunits with a high degree of accuracy. Plausible predictions for the positions of as yet unassigned proteins and RNA components are also possible. One of the conclusions derived from this separation is that 23S rRNA is solely responsible for the catalysis of peptide bond formation. Application of the separation method to any nucleoprotein complex appears feasible.

In vitro reconstitution and biophysical characterization of OEP16, an outer envelope pore protein of pea chloroplasts

More than 30% of all proteins in the living cell are membrane proteins; most of them occur in the native membranes only in very low amounts, which hinders their functional and structural investigation. Here we describe the in vitro reconstitution of overexpressed Outer Envelope Protein 16 (OEP16) from pea chloroplasts, a cation-selective channel, which has been purified from E. coli inclusion bodies. Reconstitution in detergent micelles was monitored by CD and fluorescence spectroscopy. Electron microscopy showed a homogeneous size distribution of the reconstituted protein, and differential scanning calorimetry gave an estimate of the enthalpy of protein folding. First protein crystals were obtained that have to be further refined for X-ray structural analysis. The described methods of membrane protein reconstitution and biophysical analysis might prove helpful in the study of other membrane proteins.

Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures

Molecular modeling and information processing techniques were combined to refine the structure of translocase (EF-G) in the ribosome-bound form against data from cryoelectron microscopy (cryo-EM). We devised a novel multi-scale refinement method based on vector quantization and force-field methods that gives excellent agreement between the flexibly docked structure of GDP. EF-G and the cryo-EM density map at 17 A resolution. The refinement reveals a dramatic "induced fit" conformational change on the 70S ribosome, mainly involving EF-G's domains III, IV, and V. The rearrangement of EF-G's structurally preserved regions, mediated and guided by flexible linkers, defines the site of interaction with the GTPase-associated center of the ribosome.

Alveolar epithelial barrier. Role in lung fluid balance in clinical lung injury

Several studies have established that transport of sodium from the air spaces to the lung interstitium is a primary mechanism driving alveolar fluid clearance, although further work is needed to determine the role of chloride in vectorial fluid transport across the alveolar epithelium. Although there are significant differences among species in the basal rates of sodium and fluid transport, the basic mechanism seems to depend on sodium uptake by channels on the apical membrane of alveolar type II cells, followed by extrusion of sodium on the basolateral surface by Na,K-ATPase. This process can be upregulated by several catecholamine-dependent and independent mechanisms. The identification of water channels expressed in lung, together with the high water permeabilities, suggest a potential role for channel-mediated water movement between the air space and capillary compartments, although definitive evidence will depend on the results of transgenic mouse knock-out studies. The application of this new knowledge regarding salt and water transport in alveolar epithelium in relation to pathologic conditions has been successful in clinically relevant experimental studies, as well as in a few clinical studies. The studies of exogenous and endogenous catecholamine regulation of alveolar fluid clearance are a good example of how new insights into the basic mechanisms of alveolar sodium and fluid transport can be translated to clinically relevant experimental studies. Exogenous catecholamines can increase the rate of alveolar fluid clearance in several species, including the human lung, and it is also apparent that release of endogenous catecholamines can upregulate alveolar fluid clearance in animals with septic or hypovolemic shock. It is possible that therapy with beta-adrenergic agonists might be useful to accelerate the resolution of alveolar edema in some patients. In some patients, the extent of injury to the alveolar epithelial barrier may be too severe for beta-adrenergic agonists to enhance the resolution of alveolar edema, although some experimental studies indicate that alveolar fluid clearance can be augmented in the presence of moderately severe lung injury. A longer-term upregulation of alveolar epithelial fluid transport might be achieved by strategies that accelerate the proliferation of alveolar type II cells repopulating the injured epithelium in clinical lung injury. More clinical research is needed to evaluate the strategies that can upregulate alveolar epithelial fluid transport with both short-term therapy (i.e., beta-agonists) and more sustained, longer-term effects of epithelial mitogens such as keratinocyte growth factor. These approaches may be useful in reducing mortality in the acute respiratory distress syndrome.

Trail making test, part B as a measure of executive control: validation using a set-switching paradigm

Recent controversy surrounds the use of the Trail Making Test as a measure of cognitive flexibility, given that the Trail Making Test, Part B (TMT-B) also differs from Part A (TMT-A) in factors of motor control and perceptual complexity. The present study compared performance in the TMT and a set-switching task in order to test the assumption that cognitive flexibility is captured in TMT-B performance. Set-switching tasks have low motor and perceptual selection demands, and therefore provide a clearer index of executive function. In this study, participants made category judgments for digits, letters, or symbols across a series of trials, and performance for consecutive same-task trials was compared with task-switch trials. Results of the set-switching task indicated significant switch cost, but only for the situation of task alternation (e.g., an ABA series), suggesting that task-set inhibition may play a role in this effect. Alternating-switch cost was significantly correlated with TMT-B performance, especially with the TMT-B to TMT-A ratio (B/A). Cost for alternating switches was especially large for participants with B/A ratio > 3. These results provide direct evidence that the B/A ratio of performance in the TMT provides an index of executive function.

A ratchet-like inter-subunit reorganization of the ribosome during translocation

The ribosome is a macromolecular assembly that is responsible for protein biosynthesis following genetic instructions in all organisms. It is composed of two unequal subunits: the smaller subunit binds messenger RNA and the anticodon end of transfer RNAs, and helps to decode the mRNA; and the larger subunit interacts with the amino-acid-carrying end of tRNAs and catalyses the formation of the peptide bonds. After peptide-bond formation, elongation factor G (EF-G) binds to the ribosome, triggering the translocation of peptidyl-tRNA from its aminoacyl site to the peptidyl site, and movement of mRNA by one codon. Here we analyse three-dimensional cryo-electron microscopy maps of the Escherichia coli 70S ribosome in various functional states, and show that both EF-G binding and subsequent GTP hydrolysis lead to ratchet-like rotations of the small 30S subunit relative to the large 50S subunit. Furthermore, our finding indicates a two-step mechanism of translocation: first, relative rotation of the subunits and opening of the mRNA channel following binding of GTP to EF-G; and second, advance of the mRNA/(tRNA)2 complex in the direction of the rotation of the 30S subunit, following GTP hydrolysis.

Osteomyocutaneous flap as a preclinical composite tissue allograft: swine model

Composite tissue allotransplantation (CTA) constitutes one of the last frontiers of microsurgery. Prior to its clinical application, the long-term efficacy of modern immunotherapy must be tested in a pre-clinical CTA model. Based on the concept of osteomyocutaneous forearm flap, we developed a CTA flap model in swine. After identifying the vascular territory of the flaps in six pigs (vascular casting), flaps were transplanted from mismatched donor to recipient pigs (n = 6). Rejection was assessed daily by visual inspection and histopathology of biopsy specimens. Recipient pigs were able to ambulate immediately following surgery. There were no flap failures owing to technical or surgical complications. Rejection occurred over a period of 7 days as manifested by edema, cellular infiltration, epidermalysis, and thrombosis. This pre-clinical flap model is excellent for evaluating the effectiveness of modern immunotherapy because it is anatomically and immunologically relevant and because the minimal morbidity caused to the animal permits long-term studies.

Colloidal properties of human transferrin receptor in detergent free solution

The colloidal properties of transferrin receptor, isolated from human placenta, in detergent free solution has been investigated by light scattering techniques and analytical ultracentrifugation. In detergent free solution at 293.2 K, hTfR forms stable aggregates with an apparent hydrodynamic radius of 17 nm. The molecular mass was determined by ultracentrifugation to lie between (1722+/-87) kDa (sedimentation equilibrium) and (1675+/-46) kDa (sedimentation velocity). This implies that the aggregates are build up from nine hTfR dimers. Based on model calculations, which are in good agreement with the experimental data, we propose a torus-like structure for the aggregates. Upon pH shift from pH 7.5 to 5.0 or removal of the N-linked carbohydrate chains, formation of larger aggregates is induced. These aggregates can be described in terms of porous fractal structures. We propose a simple model, which accounts for that behaviour assuming that the aggregation is mainly due to the reduction of negative surface charge.

Ischemia increases the angiogenic potency of basic fibroblast growth factor (FGF-2)

The aim of this study was to investigate the angiogenic response to exogenously administered basic fibroblast growth factor (FGF-2) in normal and ischemic skin, using the hairless mouse ear microcirculatory model. The hairless mouse ear is a well-established model for in vivo studies of skin microcirculation. Using this model, angiogenesis- and angiogenesis-associated changes in the microcirculation can be directly and continuously viewed and quantified in a variety of different experimental settings. To create ischemia in the mouse ear, all but one of the three to four feeding vessels nourishing the ear were ligated 3 days prior to a local subdermal injection of FGF-2 (9.3 + 1-0.5 mm/mm2) or saline into the dorsum of the ears. Angiogenesis was quantified by direct observation, at high magnification, of the injection site where increases in total vessel length (TVL) were measured repeatedly over 18 days following injection. We found a significant (P < 0.01) increase in TVL in normal and ischemic ears injected with FGF-2. Saline injection also induced a significant increase in TVL in ischemic ears. However, the angiogenic response to FGF-2 in ischemic ears was significantly stronger than saline alone in ischemic ears or saline or FGF-2 in normal ears. This response could be used clinically to accelerate angiogenesis and thus increase perfusion in ischemic tissue.

The ribosome--a macromolecular machine par excellence

The ribosome is the site in the cell where proteins are synthesized. Cryo-electron microscopy and X-ray crystallography have revealed the ribosome as a particle made of two subunits, each formed as an intricate mesh of RNAs and many proteins. Ligand-binding experiments followed by cryo-electron microscopy have helped to determine some of the key stages of interaction between the ribosome and the main ligand molecules.

Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 A resolution

Using a sordarin derivative, an antifungal drug, it was possible to determine the structure of a eukaryotic ribosome small middle dotEF2 complex at 17.5 A resolution by three-dimensional (3D) cryo-electron microscopy. EF2 is directly visible in the 3D map and the overall arrangement of the complex from Saccharomyces cerevisiae corresponds to that previously seen in Escherichia coli. However, pronounced differences were found in two prominent regions. First, in the yeast system the interaction between the elongation factor and the stalk region of the large subunit is much more extensive. Secondly, domain IV of EF2 contains additional mass that appears to interact with the head of the 40S subunit and the region of the main bridge of the 60S subunit. The shape and position of domain IV of EF2 suggest that it might interact directly with P-site-bound tRNA.

An immortalized rat liver stellate cell line (HSC-T6): a new cell model for the study of retinoid metabolism in vitro

Hepatocytes and hepatic stellate cells play important roles in retinoid storage and metabolism. Hepatocytes process postprandial retinyl esters and are responsible for secretion of retinol bound to retinol-binding protein (RBP) to maintain plasma retinol levels. Stellate cells are the body's major cellular storage sites for retinoid. We have characterized and utilized an immortalized rat stellate cell line, HSC-T6 cells, to facilitate study of the cellular aspects of hepatic retinoid processing. For comparison, we also carried out parallel studies in Hepa-1 hepatocytes. Like activated primary stellate cells, HSC-T6 express myogenic and neural crest cytoskeletal filaments. HSC-T6 cells take up and esterify retinol in a time- and concentration-dependent manner. Supplementation of HSC-T6 culture medium with free fatty acids (up to 300 micrometer) does not affect retinol uptake but does enhance retinol esterification up to 10-fold. RT-PCR analysis indicates that HSC-T6 cells express all 6 retinoid nuclear receptors (RARalpha, -beta, -gamma, and RXRalpha, -beta, -gamma) and like primary stellate cells, HSC-T6 stellate cells express cellular retinol-binding protein, type I (CRBP) but fail to express either retinol-binding protein (RBP) or transthyretin (TTR). Addition of retinol (10(-8)-10(-5) m) or all-trans-retinoic acid (10(-10)-10(-6) m) rapidly up-regulates CRBP expression. Using RAR-specific agonists and antagonists and an RXR-specific agonist, we show that members of the RAR-receptor family modulate HSC-T6 CRBP expression.Thus, HSC-T6 cells display the same retinoid-related phenotype as primary stellate cells in culture and will be a useful tool for study of hepatic retinoid storage and metabolism.

Identifying male college students' perceived health needs, barriers to seeking help, and recommendations to help men adopt healthier lifestyles

Seven focus groups at a university campus were formed to identify college men's health concerns, barriers to seeking help, and recommendations to help college men adopt healthier lifestyles. Content analysis was used to identify and organize primary patterns in the focus-group data. Results of the study revealed that the college men were aware that they had important health needs but took little action to address them. The participants identified both physical and emotional health concerns. Alcohol and substance abuse were rated as the most important issues for men. The greatest barrier to seeking services was the men's socialization to be independent and conceal vulnerability. The most frequently mentioned suggestions for helping men adopt healthier lifestyles were offering health classes, providing health information call-in service, and developing a men's center. Implications of the results are discussed.

Potentiometric detection of carboxylic acids, phosphate esters, and nucleotides in liquid chromatography using anion-selective coated-wire electrodes

An all-solid-state ion-selective membrane electrode incorporating a lipophilic anion exchanger was used in a flow-through potentiometric detector for the LC determination of organic anions of biological interest. Different metabolic intermediates (mono-, di-. and tricarboxylic acids, sugar phosphates, and nucleotides) were detected sensitively after separation on a pellicular anion-exchange chromatographic column. The electrode was coated by directly casting the electroactive mixture on a glassy carbon support of 3 mm diameter and used in a wall-jet-type flow cell. The analysis conditions were optimized to obtain both efficient separation and sensitive detection. Calibration curves showed a logarithmic dependence on the injected concentration for concentrations higher than 5.0 x 10(-5) M and a linear dependence for injected concentrations below this value. Under isocratic conditions, detection limits of 5.0 x 10(-7) M (25 pmol) were attained when a sodium hydroxide solution was used as an eluent. No suppressor system was needed in this case. The relative standard deviation for consecutive injections was 0.3% (n = 15), and the electrode lifetime was at least 2 months. The utility of potentiometric detection is further demonstrated in a gradient elution separation for single-run analysis of a synthetic mixture of biochemical compounds containing carboxylic acids, phosphate esters, and nucleotides.

Effects of dietary phenolic compounds on tocopherol, cholesterol, and fatty acids in rats

The effects of the phenolic compounds butylated hydroxytoluene (BHT), sesamin (S), curcumin (CU), and ferulic acid (FA) on plasma, liver, and lung concentrations of alpha- and gamma-tocopherols (T), on plasma and liver cholesterol, and on the fatty acid composition of liver lipids were studied in male Sprague-Dawley rats. Test compounds were given to rats ad libitum for 4 wk at 4 g/kg diet, in a diet low but adequate in vitamin E (36 mg/kg of gamma-T and 25 mg/kg of alpha-T) and containing 2 g/kg of cholesterol. BHT significantly reduced feed intake (P < 0.05) and body weight and increased feed conversion ratio; S and BHT caused a significant enlargement of the liver (P < 0.001), whereas CU and FA did not affect any of these parameters. The amount of liver lipids was significantly lowered by BHT (P < 0.01) while the other substances reduced liver lipid concentrations but not significantly. Regarding effects on tocopherol levels, (i) feeding of BHT resulted in a significant elevation (P< 0.001) of alpha-T in plasma, liver, and lung, while gamma-T values remained unchanged; (ii) rats provided with the S diet had substantially higher gamma-T levels (P < 0.001) in plasma, liver, and lung, whereas alpha-T levels were not affected; (iii) administration of CU raised the concentration of alpha-T in the lung (P < 0.01) but did not affect the plasma or liver values of any of the tocopherols; and (iv) FA had no effect on the levels of either homolog in the plasma, liver, or lung. The level of an unknown substance in the liver was significantly reduced by dietary BHT (P < 0.001). BHT was the only compound that tended to increase total cholesterol (TC) in plasma, due to an elevation of cholesterol in the very low density lipoprotein + low density lipoprotein (VLDL + LDL) fraction. S and FA tended to lower plasma total and VLDL + LDL cholesterol concentrations, but the effect for CU was statistically significant (P < 0.05). FA increased plasma high density lipoprotein cholesterol while the other compounds reduced it numerically, but not significantly. BHT, CU, and S reduced cholesterol levels in the liver TC (P < 0.001) and percentages of TC in liver lipids (P < 0.05). With regard to the fatty acid composition of liver lipids, S increased the n-6/n-3 and the 18:3/20:5 polyunsaturated fatty acids (PUFA) ratios, and BHT lowered total monounsaturated fatty acids and increased total PUFA (n-6 + n-3). The effects of CU and FA on fatty acids were not highly significant. These results suggest some in vivo interactions between these phenolic compounds and tocopherols that may increase the bioavailability of vitamin E and decrease cholesterol in rats.

FDG positron emission tomography in the diagnosis of peripheral pulmonary focal lesions

Positron emission tomography (PET) using fluoride-18-marked fluoride deoxyglucose (FDG) represents a metabolically based imaging technique capable of providing information on the potential malignancy of peripheral pulmonary focal lesions. In the present prospective study, we investigated the effectiveness of FDG-PET in determining the dignities of 67 such lesions in 35 patients. Findings of FDG-PET were compared with those of computed tomography (CT), as well as with surgical and histological reports, and the value of FDG-PET as a diagnostic method evaluated. FDG-PET correctly identified 38 lesions as positive for malignancy, 18 correctly as negative, 7 incorrectly as negative, and 4 incorrectly as positive. Based on lesions, this yields a sensitivity of 84.4% and a specificity of 81.8%. All malignant focal lesions with a diameter of over 1.2 cm were correctly identified (sensitivity: 100%). In cases of intense FDG uptake, differentiation between a primary lesion, a metastasis, and an acute inflammation is often not possible.

Solution structure of the E. coli 70S ribosome at 11.5 A resolution

Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows identification of RNA helices, peripheral proteins, and intersubunit bridges. Comparison of double-stranded RNA regions and positions of proteins identified in both cryo-EM and X-ray maps indicates good overall agreement but points to rearrangements of ribosomal components required for the subunit association. Fitting of known components of the 50S stalk base region into the map defines the architecture of the GTPase-associated center and reveals a major change in the orientation of the alpha-sarcin-ricin loop. Analysis of the bridging connections between the subunits provides insight into the dynamic signaling mechanism between the ribosomal subunits.

[The quality of the treatment of diabetics in kidney failure in Germany]

BACKGROUND AND OBJECTIVE

In recent years there has been a rapid increase in the number of dialysis-dependent diabetics in Germany. Survival on dialysis is not satisfactory and damage acquired in the preterminal stage of renal failure is thought to play an important role. Late referral to a nephrologist and insufficient quality of medical management are thought to contribute importantly to poor outcome. This hypothesis was evaluated in the present study.

PATIENTS AND METHOD

The data of all 173 diabetic patients (16 with type 1, 157 with type 2 diabetes, 90 men, 83 women, mean age 63.3 [31-95] years), who had been referred in 1996 for the first time to five renal units, were retrospectively assessed using a structured protocol.

RESULTS

Patients were usually referred in advanced renal failure (median creatinine clearance 29 ml/min, range 1-216) with insufficient control of systolic (170 [120-260] mmHg) and diastolic blood pressure (90 [60-180] mmHg), insufficient antihypertensive therapy (without treatment 32 of 173 patients; median number of classes of antihypertensive agents used 2 [range 1-6]; ACE inhibitors 79 of 173 patients), high HbA1c (7.9 [4.9-15.7]%) and LDL cholesterol (176 [67-307] mg/dl). Immediate dialysis was required in 45 patients.

CONCLUSION

The data document insufficient quality of treatment and late incorporation of a nephrologist into the medical team involved in the care of diabetic patients. Changes in the structure of diabetes care are necessary to improve treatment quality.

Executive control in set switching: residual switch cost and task-set inhibition

Executive processes necessary for flexibly switching between different tasks were studied using a set switching paradigm that requires participants to rapidly switch between different tasks across consecutive trials. Switch cost reflects poorer performance for task-switch trials than for consecutive same-task trials. Significant switch cost was observed even with considerable preparation time before a task-switch, an effect known as residual switch cost. This study tested the hypothesis that one process underlying residual switch cost is inhibition of the previous task-set. We used semantic categorization tasks to compare switch cost between alternating task series (ABA) and nonalternating series (ABC) in order to test the generality of a task-set inhibition effect previously observed with perceptual judgment tasks (Mayr & Keele, in press). The results yielded significant switch cost only for alternating tasks, in both response times and errors resulting from performance of the wrong task. Thus, resolving inhibition associated with previously abandoned task-sets may be the main process underlying residual switch costs, suggesting that task-set inhibition is an important executive control process.

[Diagnostic and therapeutic significance of arthroscopy in distal radius fracture]

Non-operative and minimal-invasive treatment of distal radius fractures have still a poor outcome. Although bony structures often heal acceptable, additional lesions of intraarticular ligamentous structures cause persistent pain and disability. Aim of the study was to present the diagnostic and therapeutic possibilities of arthroscopically assisted treatment of distal radius fractures. Diagnostic wrist arthroscopy found in 6 of 30 patients with distal radius fractures (23 AO type C fractures) a scapho-lunate ligament tear (20%) of which 3 had to be stabilized operatively. 18 patients (60%) presented with tears of the triangular fibrocartilage complex [Palmer classification: 1A (1); 1B (5); 1D (2); 1A, 1B (2); 1A, 1D (6); 1B, 1D (2)], which were repaired by arthroscopic shaving (n = 12), Kirschner wire stabilization of ulna head (n = 2) or arthroscopic suture (n = 3). Fractures were stabilized in most cases by combinations of canulated titan screws (3.0 mm) and Kirschner wires (n = 12). In 27 patients, the radial joint surface and the distal radio-ulnar joint could be reconstructed without any specific complications. Arthroscopic reduction of distal radius fractures allows minimal-invasive reconstruction of the joint surface, diagnoses relevant ligamentous tears and should applied with incongruencies of the joint surface greater than 2 mm and in widely dislocated fractures.

[Value of MRI in diagnosis of post-traumatic wrist complaints]

The diagnostic value of MRI in acute and chronic posttraumatic wrist pain will be demonstrated in several clinical cases. The integration of MRI in a diagnostic algorithm is discussed. The indication of MRI is given for suspected complex ligamentous lesions, occult fractures and soft tissue pathologies, in particular with disconcordant clinical and radiological signs. Pathology orientated study protocols are presented. Preoperatively, MRI will be helpful in planning definitive surgical treatment.