Cryo-electron microscopy of vitrified specimens

Cryo-electron microscopy of vitrified specimens was just emerging as a practical method when Richard Henderson proposed that we should teach an EMBO course on the new technique. The request seemed to come too early because at that moment the method looked more like a laboratory game than a useful tool. However, during the months which ellapsed before the start of the course, several of the major difficulties associated with electron microscopy of vitrified specimens found surprisingly elegant solutions or simply became non-existent. The course could therefore take place under favourable circumstances in the summer of 1983. It was repeated the following years and cryo-electron microscopy spread rapidly. Since that time, water, which was once the arch enemy of all electronmicroscopists, became what it always was in nature – an integral part of biological matter and a beautiful substance.

Intracellular targets of cyclin-dependent kinase inhibitors: identification by affinity chromatography using immobilised inhibitors

BACKGROUND

Chemical inhibitors of cyclin-dependent kinases (CDKs) have great therapeutic potential against various proliferative and neurodegenerative disorders. Olomoucine, a 2,6,9-trisubstituted purine, has been optimized for activity against CDK1/cyclin B by combinatorial and medicinal chemistry efforts to yield the purvalanol inhibitors. Although many studies support the action of purvalanols against CDKs, the actual intracellular targets of 2,6, 9-trisubstituted purines remain unverified.

RESULTS

To address this issue, purvalanol B (95. ) and an N6-methylated, CDK-inactive derivative (95M. ) were immobilized on an agarose matrix. Extracts from a diverse collection of cell types and organisms were screened for proteins binding purvalanol B. In addition to validating CDKs as intracellular targets, a variety of unexpected protein kinases were recovered from the 95. matrix. Casein kinase 1 (CK1) was identified as a principal 95. matrix binding protein in Plasmodium falciparum, Leishmania mexicana, Toxoplasma gondii and Trypanosoma cruzi. Purvalanol compounds also inhibit the proliferation of these parasites, suggesting that CK1 is a valuable target for further screening with 2,6,9-trisubstituted purine libraries.

CONCLUSIONS

That a simple batchwise affinity chromatography approach using two purine derivatives facilitated isolation of a small set of highly purified kinases suggests that this could be a general method for identifying intracellular targets relevant to a particular class of ligands. This method allows a close correlation to be established between the pattern of proteins bound to a small family of related compounds and the pattern of cellular responses to these compounds.

Linker histone-dependent DNA structure in linear mononucleosomes

We have examined the binding of the linker histone H5 (LH) to mononucleosomes. Mononucleosomes reconstituted on short DNA fragments display a series of discrete bands on a gel corresponding to various nucleosome positions along the DNA. When a series of engineered H5s with differing extents of the C-terminal tail are bound to these mononucleosomes, the electrophoretic mobilities of the resulting complexes are altered. Not only is there a general increase in mobility upon complex formation, but there is a reduction in the differences in mobility of the most distal nucleosomes. The complexes were also visualized by electronmicroscopy. From these two complementary studies, we conclude the following. (1) Entering and exiting DNAs are uncrossed in the LH-free particles, despite a DNA wrapping of 1.65 to 1.7 turns around the histone core. This results from a bending of the entering and exiting DNA away from each other and the histone surface, presumably as a consequence of electrostatic repulsion. This confirms and extends conclusions derived from our recent examination of the same particles in 3D through cryo-electron microscopy. (2) Binding of the globular domain of H5 increases DNA wrapping to 1.8 to 1.9 turns, but fails to induce a crossing due to an accentuation of the bends. (3) The C-terminal tail of H5 bridges entering and exiting DNAs together into a four-stranded stem over a distance of about 30 bp. The occurrence of such a stem may introduce constraints on models of the 30 nm chromatin fiber.

Genome-wide gene expression profiles of the developing mouse hippocampus

We have analyzed the developmental molecular programs of the mouse hippocampus, a cortical structure critical for learning and memory, by means of large-scale DNA microarray techniques. Of 11,000 genes and expressed sequence tags examined, 1,926 showed dynamic changes during hippocampal development from embryonic day 16 to postnatal day 30. Gene-cluster analysis was used to group these genes into 16 distinct clusters with striking patterns that appear to correlate with major developmental hallmarks and cellular events. These include genes involved in neuronal proliferation, differentiation, and synapse formation. A complete list of the transcriptional changes has been compiled into a comprehensive gene profile database (http://BrainGenomics.Princeton.edu), which should prove valuable in advancing our understanding of the molecular and genetic programs underlying both the development and the functions of the mammalian brain.

Molecular structure of human TFIIH

TFIIH is a multiprotein complex required for both transcription and DNA repair. Single particles of human TFIIH were revealed by electron microscopy and image processing at a resolution of 3.8 nm. TFIIH is 16 x 12.5 x 7.5 nm in size and is organized into a ring-like structure from which a large protein domain protrudes out. A subcomplex assembled from five recombinant core subunits also forms a circular architecture that can be superimposed on the ring found in human TFIIH. Immunolabeling experiments localize several subunits: p44, within the ring structure, forms the base of the protruding protein density which includes the cdk7 kinase, cyclin H, and MAT1. Within the ring structure, p44 was flanked on either side by the XPB and XPD helicases. These observations provide us with a quartenary organizational model of TFIIH.

The RNA cleavage activity of RNA polymerase III is mediated by an essential TFIIS-like subunit and is important for transcription termination

Budding yeast RNA polymerase III (Pol III) contains a small, essential subunit, named C11, that is conserved in humans and shows a strong homology to TFIIS. A mutant Pol III, heterocomplemented with Schizosaccharomyces pombe C11, was affected in transcription termination in vivo. A purified form of the enzyme (Pol III Delta), deprived of C11 subunit, initiated properly but ignored pause sites and was defective in termination. Remarkably, Pol III Delta lacked the intrinsic RNA cleavage activity of complete Pol III. In vitro reconstitution experiments demonstrated that Pol III RNA cleavage activity is mediated by C11. Mutagenesis in C11 of two conserved residues, which are critical for the TFIIS-dependent cleavage activity of Pol II, is lethal. Immunoelectron microscopy data suggested that C11 is localized on the mobile thumb-like stalk of the polymerase. We propose that C11 allows the enzyme to switch between an RNA elongation and RNA cleavage mode and that the essential role of the Pol III RNA cleavage activity is to remove the kinetic barriers to the termination process. The integration of TFIIS function into a specific Pol III subunit may stem from the opposite requirements of Pol III and Pol II in terms of transcript length and termination efficiency.

The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3

RNA polymerase I (Pol I) is dedicated to transcription of the large ribosomal DNA (rDNA). The mechanism of Pol I recruitment onto rDNA promoters is poorly understood. Here we present evidence that subunit A43 of Pol I interacts with transcription factor Rrn3: conditional mutations in A43 were found to disrupt the transcriptionally competent Pol I-Rrn3 complex, the two proteins formed a stable complex when co-expressed in Escherichia coli, overexpression of Rrn3 suppressed the mutant phenotype, and A43 and Rrn3 mutants showed synthetic lethality. Consistently, immunoelectron microscopy data showed that A43 and Rrn3 co-localize within the Pol I-Rrn3 complex. Rrn3 has several protein partners: a two-hybrid screen identified the C-terminus of subunit Rrn6 of the core factor as a Rrn3 contact, an interaction supported in vitro by affinity chromatography. Our results suggest that Rrn3 plays a central role in Pol I recruitment to rDNA promoters by bridging the enzyme to the core factor. The existence of mammalian orthologues of A43 and Rrn3 suggests evolutionary conservation of the molecular mechanisms underlying rDNA transcription in eukaryotes.

The 22q11.2 deletion: screening, diagnostic workup, and outcome of results; report on 181 patients

A submicroscopic deletion of chromosome 22q11.2 has been identified in the majority of patients with the DiGeorge syndrome, velocardiofacial syndrome, conotruncal anomaly face syndrome, and in some patients with isolated conotruncal cardiac anomalies, Opitz G/BBB syndrome, and Cayler cardiofacial syndrome. We have evaluated 181 patients with this deletion. We describe our cohort of patients, how they presented, and what has been learned by having the same subspecialists evaluate all of the children. The results help define the extremely variable phenotype associated with this submicroscopic deletion and will assist clinicians in formulating a management plan based on these findings.

Three-dimensional structures of the TAFII-containing complexes TFIID and TFTC

TBP (TATA-binding protein)-associated factors (TAF(II)s) are components of large multiprotein complexes such as TFIID, TFTC, STAGA, PCAF/GCN5, and SAGA, which play a key role in the regulation of gene expression by RNA polymerase II. The structures of TFIID and TFTC have been determined at 3.5-nanometer resolution by electron microscopy and digital image analysis of single particles. Human TFIID resembles a macromolecular clamp that contains four globular domains organized around a solvent-accessible groove of a size suitable to bind DNA. TFTC is larger and contains five domains, four of which are similar to TFIID.

En bloc resection of colon cancer adherent to other organs

This study was undertaken to determine the optimal surgical treatment of colorectal cancers with adherence to adjacent organs in the absence of distant metastases. A retrospective review of colorectal cancer at Virginia Mason Hospital from 1975 to 1979 divided patients with Dukes' stage B2 and C2 colorectal cancers into three treatment groups: standard colectomy, en bloc resection, and colectomy with separation of adherent organs, with 5 year survival rates of 55 percent, 61 percent, and 23 percent, respectively. No operative mortality occurred with en bloc resection. Survival after en bloc resection was influenced by Dukes' stage and the histologic documentation of cancer within the adherent organ. Unacceptably high local recurrence rates and poor 5 year survival rates were observed in cases where adherent organs were separated from the colorectal cancer. We conclude that colorectal cancer adherent to other organs should be treated by en bloc resection. The survival rate after en bloc resection will be comparable to the rate after standard colectomy for nonadherent colorectal cancers.

Intraventricular septations complicating neonatal meningitis

✓ Ventriculography in seven infants who had developed hydrocephalus after surviving neonatal meningitis and ventriculitis disclosed intraventricular septations or veils. These post-inflammatory septations compartmentalized the ventricular system, interfering with attempted shunting procedures. Pathogenesis and treatment are discussed.

Correlation of scoliosis and pulmonary function in Duchenne muscular dystrophy

Pulmonary function was correlated with patient age and degree of thoracic scoliosis in 25 patients with Duchenne muscular dystrophy in a retrospective, longitudinal study. The observed forced vital capacity (FVC) was found to peak at approximately the age when standing ceases, then to decline rapidly. Thoracolumbar curves were found to be insignificant in adversely affecting pulmonary function in patients with Duchenne muscular dystrophy. Percent FVC was found to be the parameter of pulmonary function that was most strongly correlated with age and scoliosis measurements. In addition, age and thoracic scoliosis together were better predictors of percent FVC than either one alone. Each 1 year of age had approximately the same negative influence on percent FVC that each 10 degrees of thoracic scoliosis had; both decreased percent FVC by approximately 4%. A regression equation for percent FVC is presented which predicts that the patient who has had scoliosis progression halted by spinal fusion would, subsequent to the surgery, show a slower rate of decline of percent FVC and that this rate is quantifiable, predictable, and dependent solely on the patient's advancing age. Therefore, early spinal instrumentation and fusion is advocated in the patient with Duchenne muscular dystrophy.

Efficient methods for attachment of thiol specific probes to the 3'-ends of synthetic oligodeoxyribonucleotides

Methodology is described for the synthesis of DNA oligomers containing a free 3'-thiol group which can be selectively crosslinked with a wide variety of probes. This chemistry is compatible with both phosphotriester and phosphoramidite solid phase chemistry. Moreover, the sulphydryl group is introduced into the 3'-nucleoside solid support linkage prior to oligonucleotide synthesis. Consequently, no additional coupling steps are required after oligonucleotide synthesis, and isolation of the 3'-thiol oligonucleotide requires only one additional deprotection step. Cross-linking of the thiol-containing oligonucleotide to a fluorescent probe was carried out with high selectivity, in high yield, and under mild conditions.

The pathomechanics of gait in Duchenne muscular dystrophy

Forty-six separate gait studies were analysed for 21 ambulatory patients with Duchenne muscular dystrophy. Three groups were defined on the basis of significant gait variables: early, transitional and late. Disease progression can be predicted with 91 per cent accuracy by three gait variables: cadence, dorsiflexion in swing, and anterior pelvic tilt. The patients in the early group manifested a positive Gower's sign but gait changes were subtle, being principally slightly increased hip flexion in swing, decreased dorsiflexion in swing and reduction in cadence. The force line moved in front of the knee center early in single-limb support. In the transitional stage, anterior pelvic tilt was exaggerated, cadence was further reduced, and foot drop in swing phase was increased. Shoulder sway was noted as a compensation for gluteus medius weakness. The base of support widened. The force line remained behind the hip joint and in front of the knee joint throughout single-limb support. In the late stage, work output increased, cadence continued to drop, shoulder sway increased further, and there was a wider base of support. The force line remained very close to the center of the hip and in front of the knee at all times during single-limb support. The authors' conclusions are: (1) the earliest postural change in gait is increased lumbar lordosis secondary to gluteus maximus weakness, and at this time the quadriceps are relatively competent; (2) quadriceps insufficiency was the key factor in gait deterioration. It appeared in the transitional stage and was characterized by exaggerated anterior pelvic tilt, restricted hip extension in stance phase, equinus posturing, and maintenance of the force line in front of the knee throughout single-limb support. Long-leg bracing is indicated when these signs of quadriceps insufficiency are noted.

Perioperative blood transfusion does not increase the risk of colorectal cancer recurrence

An adverse relationship between perioperative blood transfusions and the risk of subsequent recurrence of cancer was reported recently. We reviewed retrospectively the records of 171 patients who received initial therapy for colorectal adenocarcinoma from 1977 to 1979 at the Virginia Mason Medical Center. One hundred three patients (60%) received transfusions within 1 month of surgery and 37 patients (22%) developed recurrent cancer. No overall relationship between transfusion status (yes or no) and tumor recurrence or patient survival was found, although among subsets of patients (those with colon cancer or Dukes' Stage C2 disease), patients who had received transfusions were less likely to develop recurrent cancer than patients who had not (P = 0.01). No effect of transfusion on patient survival was found, even after consideration of potential confounding variables. The conflicting data regarding blood transfusion and cancer recurrence are reviewed, but it would appear to be premature to alter radically current blood transfusion practices based on the possibility that transfusion may adversely influence the risk of cancer recurrence.

Molecular organization of bovine rod cGMP-phosphodiesterase 6

Phosphodiesterase 6 (PDE6), a multisubunit (alphabetagamma(2)delta) enzyme, plays a major role in visual function by hydrolysing cGMP in response to a light stimulus. Solubilized bovine rod PDE6 molecules depleted of their gamma subunits were purified to homogeneity from bovine retinal rods and their molecular organization was investigated by electron microscopy. Image analysis of single particles revealed the three-dimensional dimeric arrangement of the purified alphabetadelta complex, and the internal organization of each catalytic subunit into three distinct domains at a resolution of 2.8 nm. The relative volume of each domain is consistent with sequence analysis and functional data, which suggest that these domains correspond to the catalytic and two GAF domains. This hypothesis was confirmed by immunolabelling experiments, which located the N-terminal part of the catalytic subunit where the major interaction between the two alphabeta subunits was found to occur. The 3D molecular organization of human platelet PDE5 appears highly homologous to that of bovine rod PDE6, as predicted by similarities in their primary sequences. These observations describe the quaternary organization of the catalytic PDE6 alphabeta complex, and place the catalytic and regulatory domains on a structural model.

Subhypnotic doses of thiopentone and propofol cause analgesia to experimentally induced acute pain

Subhypnotic doses of thiopentone are considered to have a hyperalgesic effect, while propofol has a hypoalgesic effect. We investigated the effect of these drugs on the nociceptive system by measuring the pain threshold to laser stimulation and the pain evoked potential (power and latency). Nineteen patients (ASA group I) participated. Twelve patients received thiopentone 0.5 mg kg-1 and propofol 0.25 mg kg-1 in random order separated by an interval of 14 h, and seven patients received saline. Immediately after the injection of both agents, the pain threshold was increased significantly (P less than 0.001) and the amplitude of the evoked potential was reduced significantly (P less than 0.05), while the latency of the evoked potential remained constant. It is concluded that, in subhypnotic doses, both thiopentone and propofol decrease the acute pain evoked by argon laser stimulation.

Diclofenac or acetaminophen for analgesia in paediatric tonsillectomy outpatients

BACKGROUND

In order to establish an effective drug regimen, we compared the analgesic efficacy of oral diclofenac and high-dose acetaminophen on pain after tonsillectomy.

METHODS

In this randomised, double-blind study 48 children, 5 to 15 years of age, following tonsillectomy were assigned to receive either diclofenac 2-3 mg kg(-1) 24 h(-1) (n=24) or acetaminophen 90 mg kg(-1) 24 h(-1) (n=24) for the first three days after surgery. Postoperative pain was assessed by self-report each day before scheduled medication at 7 h, 12 h, 18 h and 23 h.

RESULTS

The number of children rating severe pain was high in both the diclofenac group, 5-50%, and in the acetaminophen group, 12-58% during the three day study period. Pain scores in the diclofenac group were only significantly lower at 12 h on day 1-3 compared to pain scores in the acetaminophen group (P<0.05). None of the children in the diclofenac group experienced any episodes of nausea/vomiting compared to 9 children in the acetaminophen group on day 1. The incidences of nausea/vomiting increased with pain (P<0.05). None of the 48 children experienced any episodes of bleeding.

CONCLUSIONS

This study indicates that diclofenac was no more effective than high-dose acetaminophen (90 mg vs. 60 mg kg(-1) 24 h(-1)) for analgesia, but resulted in a lower incidence of nausea and vomiting in patients following tonsillectomy.

Structural analysis of a MIP family protein from the digestive tract of Cicadella viridis

Homopteran insects, and especially Cicadella viridis, display in their digestive tract a specialized epithelial differentiation, the filter chamber (FC) acting as a water-shunting complex. The main intrinsic membrane protein of the FC is a 25,000-Da polypeptide (P25). In this paper we demonstrate that this P25 polypeptide is a member of the MIP family of membrane channel proteins, and that P25 forms homotetramers in the native membranes. Using polymerase chain reaction, a 360-base pair cDNA, named cic, was isolated from RNA of the FC. cic encodes a 119-amino acid polypeptide (CIC) whose homologies with MIP26, AQP1 (CHIP), AQP2, and gamma-TIP are 38, 38, 34, and 20%, respectively. Using a specific antibody raised against a 15-amino acid peptide from the CIC sequence, we concluded that CIC and P25 are identical entities, and hence that P25 belongs to the MIP family. We investigated the quaternary structure of P25 in the membranes of the FC using biophysical analysis of P25 nondenaturing detergent micelles, scanning transmission electron microscopy, and image processing of conventional transmission electron microscopic images. All those different approaches converged to the conclusion that P25 exists as an homotetramer forming a regular two-dimensional array in the membranes.

Adrenoleukodystrophy. Electron microscopic findings

Ultrastructural and neurochemical studies were done on three male patients with adrenoleukodystrophy. In each case, the affected white matter contained enlarged glial cells filled with pathognomic intracytoplasmic inclusions consisting of electron-lucent spicules bounded by 25-Angstrom wide membranes. Similar inclusions were present in adrenocortical cells. These findings and a review of 47 reported cases indicate that adrenoleukodystrophy is a storage disorder caused by a sex-linked recessive error of metabolism.

Three-dimensional model of yeast RNA polymerase I determined by electron microscopy of two-dimensional crystals

Two-dimensional crystals of yeast RNA polymerase I dimers were obtained upon interaction with positively charged lipid layers. A three-dimensional surface model of the enzyme was determined by analyzing tilted crystalline areas and by taking advantage of the non-crystallographic internal symmetry of the dimer to correct for the missing viewing directions. The structure shows, at approximately 3 nm resolution, an irregularly shaped molecule 11 nm x 11 nm x 15 nm in size characterized by a 3 nm wide and 10 nm long groove which constitutes a putative DNA binding site. The overall structure is similar to the Escherichia coli holo enzyme and the yeast RNA polymerase II delta 4/7 structures. The most remarkable structural feature is a finger-shaped stalk which partially occludes the entrance of the groove and forms a 2.5 nm wide channel. We discuss the possible location of the catalytic centre and of the carboxy-terminal region of the beta-like subunit in the channel. The interference of different DNA fragments with RNA polymerase dimerization and crystallization indicates the orientation of the template in the putative DNA binding groove.

Spinal anaesthesia in young patients using a 29-gauge needle: technical considerations and an evaluation of postoperative complaints compared with general anaesthesia

One hundred patients aged 18-49 yr, undergoing elective arthroscopy of the knee joint, were allocated randomly to either spinal anaesthesia using a 29-gauge spinal needle or general anaesthesia. Dural puncture was considered difficult in 18% of the patients receiving spinal anaesthesia. In three patients (6%) it was necessary to supplement the spinal anaesthetic with general anaesthesia. Spinal and general anaesthesia were otherwise uneventful in all patients. The incidence of postoperative headache was similar in the two groups. One patient developed post dural puncture headache following spinal anaesthesia. This headache was of short duration and disappeared without treatment. Spinal anaesthesia caused more backache than general anaesthesia, otherwise the frequency of postoperative complaints was the same or lower. Ninety-six percent of the patients receiving spinal anaesthesia would prefer the same anaesthetic for a similar procedure in the future.

Mutagenicity of a series of hexacoordinate chromium (III) compounds

17 chromium(III) compounds have been tested for DNA-damaging capabilities using an E. coli differential repair assay and for mutagenicity in strains of Salmonella typhimurium. 4 of these compounds were active in both assays. Another 4 compounds were positive only in the repair assay and 9 were devoid of activity in both assays. Most of the doubly active complexes contain aromatic amine ligands like 2,2'-bipyridine and 1,10-phenanthroline. Closely related complexes of ligands derived from saturated amines are much less active. It appears that chromium(III) in the proper ligand environment can have considerable genetic toxicity and could represent one of the several possible ultimate species in a mechanism for chromium mutagenesis and carcinogenesis.

Onset and duration of action of rocuronium--from tracheal intubation, through intense block to complete recovery

BACKGROUND

The primary objective of this study was to establish the relation between the post tetanic count (PTC) and the time to reappearance of the first response (T1) in train-of-four (TOF) nerve stimulation following rocuronium 0.6 mg/kg, 0.9 mg/kg, and 1.2 mg/kg. The secondary objective was to evaluate the intubation conditions after 1 min.

METHODS

One hundred and eight patients were randomised to one of three doses of rocuronium: 0.6, 0.9 or 1.2 mg/kg. Tracheal intubation was performed at 60 s by a blinded investigator. During propofol, fentanyl, midazolam anaesthesia the neuromuscular block was monitored by mechanography using TOF stimulation every 12 s. At 6 min intervals, a tetanic stimulation (50 Hz) was applied for 5 s preceded and followed by a 30 s period of 1 Hz stimulation until the reappearance of T1.

RESULTS

There was a significant difference in recovery following the high dose and the two lower doses. The relation between time (min) to reappearance of T1 (t) and PTC can be expressed as follows: t(0.6 and 0.9 mg/kg)(min)=18.8-6.46 PTC and t(1.2 mg/kg)(min)=26.1-9.12 PCT. T1 was seen at a mean PTC level of 8 or 9 in all three groups. The intubation conditions were graded as excellent or good in all patients except in two patients following the 0.6 mg/kg dose of rocuronium.

CONCLUSION

The PTC method can be used to predict the time to first response to TOF nerve stimulation during intense rocuronium induced neuromuscular blockade. The relation between PTC and the time to T1 was prolonged after 1.2 mg/kg compared with 0.6 mg/kg and 0.9 mg/kg. No further improvement in intubation conditions at 60 s was evident by increasing the rocuronium dose from 0.9 mg/kg to 1.2 mg/kg.