Alignment of conduits for the nascent polypeptide chain in the ribosome-Sec61 complex

An oligomer of the Sec61 trimeric complex is thought to form the protein-conducting channel for protein transport across the endoplasmic reticulum. A purified yeast Sec61 complex bound to monomeric yeast ribosomes as an oligomer in a saturable fashion. Cryo-electron microscopy of the ribosome-Sec61 complex and a three-dimensional reconstruction showed that the Sec61 oligomer is attached to the large ribosomal subunit by a single connection. Moreover, a funnel-shaped pore in the Sec61 oligomer aligned with the exit of a tunnel traversing the large ribosomal subunit, strongly suggesting that both structures function together in the translocation of proteins across the endoplasmic reticulum membrane.

Tinkerbell--a tool for interactive segmentation of 3D data

A software system for interactive manipulation of three-dimensional data has been developed, based on the Open Inventor tool kit. The primary use of this software system is in the segmentation of tomographic reconstructions of subcellular structures. To this end, the reconstruction is represented by volume rendering and displayed in stereo. A three-dimensional cursor with adjustable shape and size is used to define and isolate regions of interest inside the volume, based on the user's expert knowledge. Once isolated, the region of interest can be conveniently analyzed and displayed.

When Gravity Fails: Local Search Topology

Local search algorithms for combinatorial search problems frequently encounter a sequence of states in which it is impossible to improve the value of the objective function; moves through these regions, called plateau moves, dominate the time spent in local search. We analyze and characterize plateaus for three different classes of randomly generated Boolean Satisfiability problems. We identify several interesting features of plateaus that impact the performance of local search algorithms. We show that local minima tend to be small but occasionally may be very large. We also show that local minima can be escaped without unsatisfying a large number of clauses, but that systematically searching for an escape route may be computationally expensive if the local minimum is large. We show that plateaus with exits, called benches, tend to be much larger than minima, and that some benches have very few exit states which local search can use to escape. We show that the solutions (i.e., global minima) of randomly generated problem instances form clusters, which behave similarly to local minima. We revisit several enhancements of local search algorithms and explain their performance in light of our results. Finally we discuss strategies for creating the next generation of local search algorithms.

Low-dose automated electron tomography: a recent implementation

Low-dose automated tomography has been implemented on a 400-kV JEOL intermediate voltage electron microscope. Instrumentation and procedures for automatic tomographic series data collection are described. Difficulties encountered and ways to overcome them are discussed. A low-dose tomographic projection series of a triad junction of frog sartorius muscle was semiautomatically collected and a 3-D reconstruction of this organelle was made.

Affinity capillary electrophoresis

The application of affinity capillary electrophoresis (ACE) to the study of molecular interactions is reviewed. ACE appears to be a sensitive, versatile and convenient tool to obtain reliable data on binding constants and stoichiometries of interacting systems using the Hummel-Dreyer method and variants thereof. A powerful feature is the possibility to analyze simultaneously the affinity of a large number of compounds for the same ligand, making it a promising tool for the screening of large combinatorial libraries.

Psychiatric disorders in elderly from the Indian sub-continent living in Bradford

In our community study of the prevalence of psychiatric disorders among elderly South Asian immigrants from the Indian sub-continent (India, Pakistan and Bangladesh) living in Bradford (UK), we found depression in 20%, dementia in 4% and anxiety neurosis in 4%. Subjects were interviewed at their place of residence by a consultant psychiatrist familiar with their culture and language. The Hindi translation of the community version of the Geriatric Mental State schedule (GMS-A) was also administered. Psychiatrist's ICD-9 diagnosis was compared with GMS-AGECAT computerized diagnosis. We found low-level agreement in dementia cases (kappa 0.33) whereas the agreement in subjects with depression was high (kappa 0.81). In many subjects GMS-A made a diagnosis of dementia not diagnosed as cases by the psychiatrist, who had the benefit of additional history information from carers in this population from a different culture and educational background. These findings are discussed along with suggestions and present limitations of GMS-A in the diagnosis of dementia in cross-cultural research. Larger studies are needed in this population (a) to find out prevalence rates in countries of origin and (b) to investigate the author's (KB) observation of low rates of Alzheimer's type dementia in this population, which may have aetiological significance.

The IMIA WG1 database on health and medical informatics programs and courses: a call for participation

Working Group 1 on health and medical informatics education of the International Medical Informatics Association (IMIA) has established a WWW site (http:/(/)ix.urz.uni-heidelberg.de/-d16) to provide up-to-date information about its work. The core of the site is an underlying database providing information on health and medical informatics (HMI) programs and courses worldwide. To be able to have a database of high quality and value we encourage all teachers and institutions to submit information about courses and programs on HMI education offered and to set pointers to their own WWW sites. In addition, a mailing list was installed to facilitate communication between all persons interested in HMI education. For subscription a message has to be sent to "listserv@listserv.net". The body of the message should read "SUBSCRIBE IMIA-WG1". Messages to the IMIA WG1 list have to be sent to "imia-wg1@urzinfo.urz.uni-heidelberg.de".

Effect of lipoteichoic acid on thermotropic membrane properties

Lipoteichoic acid, diglucosyldiacylglycerol, and phosphatidylglycerol isolated from Staphylococcus aureus were embedded in dipalmitoylglycerophosphoglycerol vesicles, and their thermotropic influence on this matrix was studied by differential scanning calorimetry. The natural fatty acids of phosphatidylglycerol effected peak broadening and a decrease in molar heat capacity. These effects were more pronounced with the glycolipid, which also increased the main transition temperature. With the lipoteichoic acid mixtures, two broad main transition peaks were observed, possibly due to different levels of lipoteichoic acid in vesicles. Both peaks showed a further upshift in transition temperatures and a pronounced decrease in molar heat capacity. Since the diacylglycerol moieties of all three amphiphiles were practically identical, the differences in the thermotropic effects have to be ascribed to the different structures of the head groups. Diglucosyldiacylglycerol is proposed to exert an additional effect by hydrogen bonding the hydroxyls of the sugar rings to their phospholipid neighbors. The stronger effect of lipoteichoic acid points to dynamic interactions of the long hydrophilic chain with the vesicle surface, which stabilize the membrane structure.

Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome

Cryoelectron microscopy provides the means of studying macromolecules in their native state. However, the contrast transfer function (CTF) makes the images and the three-dimensional (3D) maps derived from them difficult to interpret. We developed methods to determine the CTF from experimental data and to obtain a CTF-corrected 3D reconstruction. The CTF correction and 3D reconstruction accomplished in one step make it easy to combine different defocus data sets and decrease the error accumulation in the computation. These methods were applied to energy-filtered images of the 70S Escherichia coli ribosome, resulting in a distortion-free 3D map of the ribosome at 1/24.5 A-1 resolution, as determined by the differential phase residual resolution criterion.

The ribosome at higher resolution--the donut takes shape

Major new results in the 3D cryoimaging of ribosomes have advanced our understanding of ribosomal structure and function. For the first time, 3D difference maps have been used to image tRNA molecules in situ. With this new technology, the stage is set for detailed ligand-binding experiments that explore the binding states of elongation factors and tRNA, and that pinpoint locations of proteins and RNA on the surface of the ribosome.

[A new method of ex vivo whole blood perfusion of isolated mammalian organs, exemplified by the kidney of swine]

A new method for the ex vivo perfusion of organs from large mammals is described. Gas exchange and dialysis are carried out simultaneously with a low-flux polysulfon dialysis module. The dialysate (e.g. Tyrode solution) is aerated with a mixture of oxygen and carbon dioxide to ensure gas exchange with the blood. Dialysis is carried out in a closed thermostatically controlled system. Monitoring of ultrafiltration is maintained by continuously weighing the blood reservoir and adjusting an afferent and efferent blood pump. Initial results obtained with isolated pig kidneys demonstrate the suitability of the new method for use as a model for the replacement of animal experiments. Theoretically, clinical application in the area of in vivo regional organ perfusion may also be possible.

Properties of an NAD(H)-containing methanol dehydrogenase and its activator protein from Bacillus methanolicus

Oxidation of C1-C4 primary alcohols in thermotolerant Bacillus methanolicus strains is catalyzed by an NAD-dependent methanol dehydrogenase (MDH), composed of ten identical 43,000-Mr subunits. Each MDH subunit contains a tightly, but non-covalently, bound NAD(H) molecule, in addition to 1 Zn2+ and 1-2 Mg2+ ions. The NAD(H) cofactor is oxidized and reduced by formaldehyde and methanol, respectively, while it remains bound to the enzyme. Incubation of MDH with methanol and exogenous NAD (coenzyme) results in reduction of this NAD coenzyme. Both NAD species are not exchanged during catalysis. NAD thus plays two different and important roles in the MDH-catalyzed reaction, with the bound NAD cofactor acting as primary electron acceptor and the NAD coenzyme being responsible for reoxidation of the reduced cofactor. MDH obeys a ping-pong type reaction mechanism, which is consistent with such a temporary parking of reducing equivalents at the MDH-bound cofactor. Spectral studies show that, in the presence of exogenous NAD and Mg2+ ions, MDH interacts with a previously identified 50,000-Mr activator protein. The activator protein appears to facilitate the oxidation of the reduced NADH cofactor of MDH, which results in a strongly increased turnover rate of MDH.

Direct localization of the tRNAs within the elongating ribosome by means of neutron scattering (proton-spin contrast-variation)

A new technique for neutron scattering, the proton-spin contrast-variation, improves the signal-to-noise ratio more than one order of magnitude as compared to conventional techniques. The improved signal enables small RNA ligands within a large deuterated ribonucleic acid-protein complex to be measured. We used this technique to determine the positions of the two tRNAs within the elongating ribosome before and after translocation. Using a four-sphere model for each of the L-shaped tRNAs, unequivocal solutions were found for the localization of the mass centre of both tRNAs. The centre of gravity is located in the interface cavity separating the ribosomal subunits near the neck of the 30 S subunit. It moves during translocation by 12(+/-4) A towards the head of the 30 S subunit and slightly towards the L1 protuberance of the 50 S subunit.