Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology

We present a method for condensing the information in multiple alignments of proteins into a mixture of Dirichlet densities over amino acid distributions. Dirichlet mixture densities are designed to be combined with observed amino acid frequencies to form estimates of expected amino acid probabilities at each position in a profile, hidden Markov model or other statistical model. These estimates give a statistical model greater generalization capacity, so that remotely related family members can be more reliably recognized by the model. This paper corrects the previously published formula for estimating these expected probabilities, and contains complete derivations of the Dirichlet mixture formulas, methods for optimizing the mixtures to match particular databases, and suggestions for efficient implementation.

Detection of group C rotavirus in infants with extrahepatic biliary atresia

The purpose of this retrospective study was to examine liver tissue from patients with cholestatic disease for the presence of group C rotavirus RNA. The reverse transcriptase-polymerase chain reaction (PCR) for genes 5 and 6 was used, and the PCR products were subjected to liquid hybridization with a 32P-labeled probe. A second amplification with nested primers was also used. Samples from 32 subjects (20 with biliary atresia or choledochal cyst and 12 controls) were tested. Ten of 20 biliary atresia patients were positive for group C rotavirus RNA; no controls were positive (P < .003). Three of the positive patients were positive for both genes 5 and 6. Six of the 10 had > 1 sample that was positive. These data suggest a possible relationship between group C rotavirus and extrahepatic biliary atresia in the 10 patients in whom virus RNA was detected.

Pain palliation with strontium-89 in children with metastatic disease

We report two cases of children with metastatic bone disease who received strontium-89 intravenously. An 11-year-old boy with stage IV neuroblastoma received 50 microCi/kg of strontium-89. He had a good response, and his pain abated to the point that he could be taken off IV Dilaudid and was discharged from the hospital. A 7-year-old girl with the diagnosis of squamous cell carcinoma of the lung disclosed minimal increased uptake on a bone scan. Following the strontium-89 therapy, she did not have any significant improvement in pain, probably due to the minimal osteoblastic activity evidenced by the minimal abnormalities on the bone scan. Until this report there has been no reported case of using strontium-89 in the treatment of children with metastatic disease.

Localization of anti-CENP antibodies and alphoid sequences in acentric heterochromatin in a breast cancer cell line

Karyotype alterations are a hallmark of cancer cells. Of particular interest to our laboratory are the inactive centromeres and blocks of heterochromatin devoid of the accompanying centromere. When purified or monospecies anticentromere proteins (CENP) antibodies or the whole serum from scleroderma (crest) patients are applied to human chromosomes, the centromere region exhibits the label. When we treated MDA 435 cells with the anti-CENP-A, anti-CENP-B, or the whole serum, the label was apparent on heterochromatin pericentric to the active and inactive centromeres. Moreover, blocks of heterochromatin not associated with any centromere also exhibited the label. Anti-CENP-C, however, is more strictly confined to the centromere in discrete dots and is not detected on any region except the sites of active centromeres. Distribution of alpha sequences also shows a pattern compatible with its distribution in the heterochromatin. Apparently, the use of anti-CENP-A and anti-CENP-B antibodies or alphoid DNA may not detect either the centromere (primary constriction) or the kinetochore; CENP-C may be an exception.

Tolerance of single, but not multiple, amino acid replacements in antibody VH CDR 2: a means of minimizing B cell wastage from somatic hypermutation?

Mutations in the heavy chain complementarity determining region 2 (CDR2) of the phosphocholine-specific T15 Ab can have a dramatic effect on the ability of the Ab to bind Ag. A panel of multisite mutants that had lost detectable binding to phosphocholine-containing Ags was previously created by saturation mutagenesis of the CDR2 region of T15. Based on the predicted importance of amino acid changes represented in the multisite mutants, we have created single-site mutations, yielding a panel of Abs with which to test 17 of the 19 CDR2 residues. Of the 17 positions examined, only one, Arg52, is intolerant to change, yielding a nonbinder phenotype even with conservative amino acid replacement. Mutation at two other sites, Ala50 and Tyr55, can yield a nonbinder phenotype depending on the amino acid replacement. Single-site mutations of the remaining 14 positions allowed retention of binding ability. Thus, except for positions 50, 52, and 55, multiple mutations must be introduced into the CDR2 region to create a nonbinder phenotype. We provide a newly refined model of T15, illustrating the structure and the interactions of the CDR2 region. Our results imply that introduction of point mutations would not normally delete Ag-binding ability until two or more mutations had accumulated. This would minimize potentially harmful effects of somatic mutation on Ig V region genes and improve the chance of survival for an Ab such as T15, which in its unmutated form is already well suited to bind Ag.

Tolerance of single, but not multiple, amino acid replacements in antibody VH CDR 2: a means of minimizing B cell wastage from somatic hypermutation?

Mutations in the heavy chain complementarity determining region 2 (CDR2) of the phosphocholine-specific T15 Ab can have a dramatic effect on the ability of the Ab to bind Ag. A panel of multisite mutants that had lost detectable binding to phosphocholine-containing Ags was previously created by saturation mutagenesis of the CDR2 region of T15. Based on the predicted importance of amino acid changes represented in the multisite mutants, we have created single-site mutations, yielding a panel of Abs with which to test 17 of the 19 CDR2 residues. Of the 17 positions examined, only one, Arg52, is intolerant to change, yielding a nonbinder phenotype even with conservative amino acid replacement. Mutation at two other sites, Ala50 and Tyr55, can yield a nonbinder phenotype depending on the amino acid replacement. Single-site mutations of the remaining 14 positions allowed retention of binding ability. Thus, except for positions 50, 52, and 55, multiple mutations must be introduced into the CDR2 region to create a nonbinder phenotype. We provide a newly refined model of T15, illustrating the structure and the interactions of the CDR2 region. Our results imply that introduction of point mutations would not normally delete Ag-binding ability until two or more mutations had accumulated. This would minimize potentially harmful effects of somatic mutation on Ig V region genes and improve the chance of survival for an Ab such as T15, which in its unmutated form is already well suited to bind Ag.

Differential effects of reduced muscle use (hindlimb unweighting) on skeletal muscle with aging

The changes in hindlimb muscle mass, fiber area and contractile tension that occurred with two weeks of reduced weight-bearing (HU) were of greater magnitude in 6-month-old as opposed to 36-month-old rats. The pattern of change following HU for young and old animals differed, which may indicate that multiple mechanisms are responsible for the observed changes. The majority of old rats had difficulty with ambulation following unweighting, suggesting that the functional consequences of reduced weight-bearing are greater in old than in young animals. One hour of weight-bearing during HU attenuated the decline in SOL fiber atrophy, muscle mass and Po, but had no apparent effect on the GAST, PL or EDL. The reduction in Po with HU was not due, except for the old PL, to changes at the neuromuscular junction.

Analysis of the relationship between the decrease in pH and accumulation of 3-phosphoglyceric acid in developing forespores of Bacillus species

Analysis of the pH decrease and 3-phosphoglyceric acid (3PGA) accumulation in the forespore compartment of sporulating cells of Bacillus subtilis showed that the pH decrease of 1 to 1.2 units at approximately 4 h of sporulation preceded 3PGA accumulation, as observed previously in B. megaterium. These data, as well as analysis of the forespore pH decrease in asporogenous mutants of B. subtilis, indicated that sigma G-dependent forespore transcription, but not sigma K-dependent mother cell transcription, is required for the forespore pH decrease. Further analysis of these asporogenous mutants showed an excellent correlation between the forespore pH decrease and the forespore's accumulation of 3PGA. These latter results are consistent with our previous suggestion that the decrease in forespore pH results in greatly decreased activity of phosphoglycerate mutase in the forespore, which in turn leads to 3PGA accumulation. In further support of this suggestion, we found that (i) elevating the pH of developing forespores of B. megaterium resulted in rapid utilization of the forespore's 3PGA depot and (ii) increasing forespore levels of PGM approximately 10-fold in B. subtilis resulted in a large decrease in the spore's depot of 3PGA. The B. subtilis strain with a high phosphoglycerate mutase level sporulated, and the spores germinated and went through outgrowth normally, indicating that forespore accumulation of a large 3PGA depot is not essential for these processes.

Binding of phenylphosphocholine-carrier conjugates to the combining site of antibodies maintains a conformation of the hapten

The structural basis of the binding of phenylphosphocholine haptens to antibodies was studied. This was done by preparing antibodies and testing binding to conjugates of phenylphosphocholine. The choice of haptens was made in order to evaluate the contribution of the carrier to binding, and its effect on hapten conformation in the active site. Thus, phosphocholine (PC) was diazophenyl-linked to tyrosine or histidine as single amino acid carriers and to tripeptides or octapeptides containing tyrosine or histidine as central amino acids to which PC was attached. Relative affinity was assessed by inhibition enzyme-linked immunosorbent assay (ELISA) and binding constants were determined by fluorescence quenching. Fluorinated haptens were used to determine the kinetics of binding using 19F nuclear magnetic resonance. The transferred nuclear Overhauser effect was used to characterize conformation of the bound hapten. We had previously shown that nitrophenylphosphocholine unlinked to carrier is bound in the active site as a bent structure [Bruderer, U., Peyton, D. H., Barbar, E., Fellman, J. H., & Rittenberg, M. B. (1992) Biochemistry 31, 584-589]. We show here that this same bent conformation is retained in the active site regardless of the neighboring carrier or the conformation of the hapten in the unbound conjugate. The presence of the carrier residues in the bound state does, however, influence affinity.

Drug therapy in multiple sclerosis: a study of Nova Scotia senior citizens

We conducted a study to determine the types and costs of drugs used by Nova Scotia senior citizens with multiple sclerosis (MS) compared with the types and costs of drugs used by all senior citizens in Nova Scotia. Administrative claims databases from the Nova Scotia Seniors Pharmacare program for persons aged 65 years or older were linked to the Dalhousie Multiple Sclerosis Research Unit (DMSRU) clinical database (1980-1994). Analyses compared persons with MS aged 65 years or older who attended the DMSRU at least once with the general population of senior citizens. Not all persons with MS attended the DMSRU. In aggregate, Pharmacare costs in 1993-1994 for patients with MS aged 65 years or older (N = 52) were $975.00 Canadian per capita compared with $590.00 Canadian for all senior citizens in Nova Scotia (N = 108,646). Thus average drug costs for the senior citizens with MS were 65% greater than those for all senior citizens covered by Nova Scotia's comprehensive, publicly funded Pharmacare program. Compared with other senior citizens, those with MS more frequently received alpha-blockers, anticholinergics, cholinergics, tricyclic antidepressants, anticonvulsants, antifatigue agents, antispasticity agents, and antibiotics for bladder infections.

A phase III randomized prospective trial of external beam radiotherapy, mitomycin C, carmustine, and 6-mercaptopurine for the treatment of adults with anaplastic glioma of the brain. CNS Cancer Consortium

PURPOSE

This study was designed to evaluate strategies to overcome the resistance of anaplastic gliomas of the brain to external beam radiotherapy (ERT) plus carmustine (BCNU). Patients were > or = 15 years of age, had a histologic diagnosis of malignant glioma, and a Karnofsky performance status (KPS) > or = 60%.

METHODS AND MATERIALS

In Randomization 1, patients were assigned to receive either ERT alone (61.2 Gy) or ERT plus mitomycin C (Mito, IV 12.5 mg/m(2)) during the first and fourth week of ERT. After this treatment, patients went on to Randomization 2, where they were assigned to receive either BCNU (i.v. 200 mg/m(2)) given at 6-week intervals or 6-mercaptopurine (6- MP, 750 mg/m(2) IV daily for 3 days every six weeks), with BCNU given on the third day of the 6-MP treatment. Three hundred twenty-seven patients underwent Randomization 1. One hundred sixty-four received ERT alone, and 163 received ERT + Mito [average 52.7 years; 63% male; 69% glioblastoma multiforme (GBM); 66% had a resection; 56% KPS > or = 90%]. Step-wise analysis of survival from Randomization 1 or 2 indicates that survival was significantly diminished by: (a) age > or = 45 years (b) KPS < 90%; (c) GBM/gliosarcoma histology; (d) stereotactic biopsy as opposed to open biopsy or resection. Median survival from Randomization 1 in both arms (ERT + Mito) was 10.8 months. Median survival from Randomization 2 was 9.3 months for BCNU/6MP vs. 11.4 months for the BCNU group (p = 0.35). Carmustine/6-MP showed a possible survival benefit for histologies other than GBM/GS. Two hundred and thirty-three patients underwent Randomization 2. The proportion of patients in the ERT group who terminated study prior to Randomization 2 was significantly less in the ERT group than in the ERT + Mito group (20 vs. 37%, p < 0.001).

CONCLUSIONS

(a) The addition of Mito to ERT had no impact on survival; (b) patients treated with ERT + Mito were at greater risk of terminating therapy prior to Randomization 2; (c) there was not a significant survival benefit to the addition of 6-MP to BCNU.

Measurement of dynamic pressures at the shoe-foot interface during normal walking with various foot orthoses using the FSCAN system

Foot orthoses are routinely used in clinical practice to redistribute pressure at the shoe-foot interface, although there is very little scientific evidence to support the efficacy of their use. In this study, the FSCAN sensor (an ultrathin in-shoe transducer) was used to determine the efficacy of pressure redistribution with a Plastizote, Spenco, cork, and a plastic foot orthosis as compared with control (no orthosis). Measurement variations of up to 18% occurred between sensors, and changes in stance time of up to 5% occurred between the orthoses and the control conditions. In spite of these potentially confounding variables, statistically significant differences in peak pressure between the orthotic types and the control condition (range, 9-146%) were noted. We conclude that Plastizote, cork, and plastic foot orthoses can be beneficial in relieving pressure in certain regions of the shoe-foot interface, but that they may do so at the cost of increasing pressure in other areas of the plantar surface.

Complexity of age-related change in skeletal muscle

Age-related changes in skeletal muscle mass, fiber area, and contractile function were examined in pathogen-free rats at 6, 12, 28 and 36 mos of age. The intent of this study was to clarify age-related decline, particularly in contractile force, and to determine if the decline in contractile tension with age is due to alterations at the neuromuscular junction. A variable amount of age-associated reduction in muscle mass was noted for the soleus (18%), extensor digitorum longus (EDL-16%), plantaris (37%), and gastrocnemius (38%) muscles. The decline in fiber area for these four muscles was between 5 and 16% greater than the loss in muscle wet weight. A variable amount of change in peak contractile force between 6 and 36 mos was observed for the soleus (62%), EDL (48%), and plantaris (34%). For soleus and EDL, the decline in peak tetanic tension exceeded the decline in muscle mass and fiber area. Most of the declines for the animals used in this study did not become significant until after the age of 28 mo. The marked reduction in peak tetanic tension, fiber area, and muscle mass between 28 and 36 mos indicates an accelerated age-related decline in this time period. The reduced peak twitch and peak tetanic tension in the oldest animals was not due to likely age-related changes at the neuromuscular junction. Peak values for tetanic tension were similar, whether tension was elicited via direct muscle stimulation or through stimulation of the nerve. Results underscore the complexity of age-related change and suggest that multiple mechanisms contribute to the decline of skeletal muscle.

A man with "shrub leg"

A 39-year-old man with confirmed HIV infection of six years' duration presented with painful swelling of his right lower leg. Two weeks earlier, he had scratched the leg on a shrub.

Structural features unique to enteric adenoviruses

Enteric adenoviruses are important agents of pediatric gastroenteritis. Characterization of monoclonal antibodies against human adenovirus 41 (h-41) identified an epitope of interest on protein VI, an internal virion protein. The epitope is common to enteric adenoviruses (subgenus A: h-12, h-18, h-31 and subgenus F: h-40, h-41) but is not shared by non-enteric serotypes (subgenera B, C, D or E). By expressing random oligonucleotide fragments of the protein VI gene as T7 gene 10 fusion proteins in the pTope vector (Novagen), the epitope was mapped within the central domain of protein VI, to the region corresponding to aa 114-125 of the Ad2 protein. Identification of this epitope reflects the close evolutionary relationship of subgenus A and subgenus F adenoviruses and draws attention to structural features of enteric adenoviruses as potential determinants of tropism. Furthermore, this epitope may be valuable for identification of enteric adenoviruses in clinical specimens.

Neural network modeling of the hippocampal formation spatial signals and their possible role in navigation: a modular approach

Cells throughout the hippocampal formation show striking spatial firing correlates as a rat navigates through space. These cells are thought to play a critical role in orchestrating the navigational abilities of the animals, since damage to the hippocampal formation causes spatial learning deficits. Here, we present a theoretical framework aimed at explaining how the different spatial signals are generated, as well as how they may help guide navigational behavior. Earlier work from our laboratory has presented a simple model for how the location-related signals exhibited by hippocampal place cells could be generated, based on convergent sensory information. Here, the results of this work are combined with two more recent models, to provide a more comprehensive theoretical framework. Specifically, we present 1) A neural network model of head direction cells, based on the idea that the directional signals are generated using a path integration mechanism. Cells which combine directional and angular head velocity information project onto the head direction cells, to "update" the current directional signal. This model reproduces the basic phenomenon of direction-specific firing, as well as the anticipatory nature of this firing, reported for some head direction cells. 2) A network simulation of how the hippocampal spatial signals could be used to orchestrate instrumental learning. Here, place and directional signals converge onto motor cells, each of which are thus driven to fire to specific combinations of location and directional heading. Each active motor cell generates a small leftward or rightward "step" of the simulated animal. When the simulated goal is encountered, recently active synapses are strengthened, so that goal-directed trajectories are "stamped in". We have found these models useful in helping to clarify our thinking about the proposed theoretical principles, as well as in generating testable predictions.