Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium.

The current status and future outlook of macromolecular structure databases and information handling, with particular reference to European databases, are reviewed. Issues concerning the efficiency with which data are represented, validated, archived and accessed are discussed in view of the fast growing body of information on structures of biological macromolecules.

Discography of lumbar discs after surgical treatment for disc herniation.

STUDY DESIGN: Eighty-three patients were identified who had discography performed at a disc level that had been subject to previous laminectomy and partial discectomy, and who had also undergone discography at one or more additional levels. The results of these studies were retrospectively reviewed. OBJECTIVE: To define the results of discography performed on previously operated discs. SUMMARY OF BACKGROUND DATA: It is not uncommon for the physician to encounter patients with complaints of persistent chronic back pain after surgical treatment of a lumbar disc herniation. Although such patients are frequently studied by discography, there is very little scientific literature to document the expected results. METHODS: A retrospective study of the results of discography on previously operated disc was performed. RESULTS: A positive pain response was significantly more likely in the previously operated discs than in the unoperated discs (P < 0.0001). Posterior extravasation of dye was noted in 34% (35 of 102) of the postoperative discs and 21% (29 of 136) of the unoperated discs. Positive concordant pain provocation was noted in 48 (75%) of the 64 discs showing posterior dye extravasation; 28 were postoperative discs and 20 were unoperated discs. CONCLUSIONS: Patients presenting with disabling back pain who had previously undergone surgical treatment for a herniated nucleus pulposus show a high (72%) incidence of concordant pain with discography of the previously operated level. Only 34% of the previously operated discs demonstrated posterior extravasation of discography dye. Persistence of a posterior anular defect was associated with a higher incidence of positive concordant pain response.

Augmenting local bone with Grafton demineralized bone matrix for posterolateral lumbar spine fusion: avoiding second site autologous bone harvest.

Mineralization and integrity of the bone graft mass were evaluated among patients having posterolateral fusion. Grafting consisted of a composite of Grafton and "local" autologous bone (n=56) or iliac crest autograft alone (n=52). Mineralization was rated radiographically at baseline and at 3, 6, 12, and 24 months. Integrity was judged as fused or not fused. Mineralization ratings did not differ significantly between groups at any postoperative interval (P values of .25-1.00). The percentage of patients fused was similar in both groups (60% and 56% for Grafton and controls, respectively; P=.83). Fifteen control patients reported donor site pain. These findings warrant further evaluation of this composite.

Efficacy of FIT produce wash and chlorine dioxide on pathogen control in fresh potatoes.

A commercial fresh pack potato operation was used as a model to evaluate FIT fruit and vegetable wash effectiveness in reducing levels of microorganisms on potatoes and in flume water. Fresh potatoes were washed in flume water with or without FIT, or treated with a spray bar utilizing either FIT, 9 ppm chlorine dioxide (CIO2), or a water control. Both flume treatments were also evaluated for APC and Gram-negatives. There were no significant differences in reduction of these microorganisms on treated or control potatoes. However, levels of Gram-negative bacteria in FIT-amended flume water were reduced by 5.95 log CFU/g, and the APC was reduced by 1.43 log CFU/g. To validate plant trial findings, this test was repeated using solutions of sterile potato flume water from the fresh pack operation, containing a typical level of dissolved and suspended solids. Treatment solutions prepared with flume water or deionized water containing FIT, 9 ppm CIO2, or a water control were inoculated with E. coli O157:H7, Salmonella Typhimurium, or Pectobacterium carotovorumssp. carotovorum. FIT and ClO2 prepared with deionized water reduced levels of microorganisms by >6.1 to 6.6 log CFU/g to below the detection limit. FIT prepared with flume water reduced levels of all organisms by >6.0 to 6.4 log CFU/g to below the detection limit, whereas ClO2 prepared from flume water reduced bacterial levels of all organisms by only 0.7 to 1.4 log CFU/g. Neither FIT nor ClO2 was particularly efficacious against E. coli O157:H7, S. Typhimurium, APC, yeasts, or molds on potato surfaces.

Aerosolization as novel sanitizer delivery system to reduce food-borne pathogens.

AIMS: As a preliminary experiment on new sanitizer delivery tools, the efficacy of aerosolized sanitizer on food-borne pathogens was investigated in larger model chamber system. METHODS: Peroxyacetic acid and hydrogen peroxide were aerosolized in a model system against artificially inoculated target micro-organisms on laboratory media. Cultures of four different food-borne pathogens were inoculated and affixed onto three different heights (bottom, wall and ceiling), and three different orientations (face-down, vertical and face-down) inside a commercial semi-trailer cabinet (14.6 x 2.6 x 2.8 m). Sanitizer was aerosolized into 2 microm droplet size fog and treated for 1 h at ambient temperature. RESULTS: Populations of Bacillus cereus, Listeria innocua, Staphylococcus aureus, and Salmonella typhimurium were reduced by an average of 3.09, 7.69, 6.93 and 8.18 log units per plate respectively. Interestingly, L. innocua, Staph. aureus, and Salm. typhimurium showed statistically not different (P >/= 0.05) reduction patterns relative to height and orientation that were never expected in a spraying system. CONCLUSIONS: Aerosolized sanitizers diffuse like gaseous sanitizers. SIGNIFICANCE AND IMPACT OF THE STUDY: Aerosolization has great potential for use in commercial applications.

Finding hydrophobic microdomains using an object-oriented database.

A procedure for finding clusters of adjacent residues in protein hydrophobic cores--hydrophobic microdomains--has been proposed by Plochocka et al. A program is presented that finds hydrophobic microdomains, making use of protein structure data stored in an object-oriented database and the list-processing features of Prolog. Alternative definitions for hydrophobic microdomains are explored. Results are presented for haemoglobin.

The correlation method for rapid monitoring of Escherichia coli in foods.

AIMS: A new rapid method was developed to rapidly monitor Escherichia coli counts in foods. MATERIALS AND RESULTS: One ml of modified selective broth with 4-methylumbelliferyl beta-D-glucuronide and 1 ml of food sample were mixed in a sterile test tube and incubated at 37 degrees C. The positive reaction (fluorescence under u.v. light) was monitored at regular 30 min intervals. The positive reaction times in test tubes were compared with actual E. coli numbers from tested samples. The growth of E. coli in test tubes (broth) was much faster than growth on agar. The first experiment was performed to evaluate the rapid correlation method using pure E. coli cultures. The correlation between E. coli counts by the conventional plating method and positive reaction (fluorescence production) times in test tubes was highly agreeable (r(2) = 0 x 95). In the case of low E. coli numbers, such as 2 x 0 log10 cfu ml(-1), the rapid correlation method detected their presence after 10 h incubation. When highly contaminated samples were assayed (8 log10 cfu ml(-1)), the rapid correlation method detected the presence of E. coli after 4 h incubation. In the ground beef experiment, the correlation between fluorescence production time and actual E. coli numbers was also strongly agreeable (r(2) = 0 x 92). CONCLUSIONS: From these results, it is obvious that the new rapid method can rapidly monitor E. coli counts in foods. SIGNIFICANCE AND IMPACT OF THE STUDY: The results indicated that the new method saved about 10-14 h incubation time compared to conventional plating methods. The rapid correlation method required much shorter incubation times compared to conventional plating methods for monitoring E. coli.

A constraint-based assignment system for automating long side chain assignments in protein 2D NMR spectra.

The sequential assignment of protein 2D NMR data has been tackled by many automated and semi-automated systems. One area that these systems have not tackled is the searching of the TOCSY spectrum looking for cross peaks and chemical shift values for hydrogen nuclei that are at the end of long side chains. This paper describes our system for solving this problem using constraint logic programming and compares our constraint satisfaction algorithm to a standard backtracking version.

Upper genital tract changes associated with exposure in utero to diethylstilbestrol.

Hysterosalpingograms of 60 young women exposed in utero to diethystilbestrol were obtained. In 46 instances, documentation of this exposure was obtained from the mother's chart review or confirmed by the attending physician. In 14 instances, the patients' mothers were sure they had received stilbestrol, but documentation could not be specifically confirmed. Hysterosalpingograms of 23 women being investigated for infertility during the same period that the current study was conducted were also reviewed. In 40 women exposed to stilbestrol, changes in the uterus which differed significantly from those seen in the past in nonexposed individuals were noted. These changes consisted of a 'T-shaped appearance of the uterus,' constricting bands in the uterine cavity, a hypoplastic uterus, and less frequently, intrauterine polypoid defects, synechiae, and in one instance a unicornuate uterus. In 36 of the 40 women gross defects were also noted in the cervix. By comparison, in none of the control subjects were defects noted which could be considered comparable with those seen in the DES-exposed patient.

PIP: Hysterosalpingography was employed to study 60 young women who were exposed in utero to diethylstilbestrol (DES). Exposure to DES was documented in 46 cases. 40 subjects exposed to DES displayed a ''T-shaped appearance of the uterus,'' constricting bands in the uterus, hypoplastic uterus, and in some cases, intrauterine polyploid defects, synechiae, and a unicornate uterus. 36 of these women also showed gross defects of the cervix. In contrast, none of the infertile control subjects exhibited defects comparable in degree to those observed in the subjects exposed to DES in utero.

An object-oriented database for protein structure analysis.

An object-oriented database system has been developed which is being used to store protein structure data. The database can be queried using the logic programming language Prolog or the query language Daplex. Queries retrieve information by navigating through a network of objects which represent the primary, secondary and tertiary structures of proteins. Routines written in both Prolog and Daplex can integrate complex calculations with the retrieval of data from the database, and can also be stored in the database for sharing among users. Thus object-oriented databases are better suited to prototyping applications and answering complex queries about protein structure than relational databases. This system has been used to find loops of varying length and anchor positions when modelling homologous protein structures.

A novel CD8-independent high-avidity cytotoxic T-lymphocyte response directed against an epitope in the phosphoprotein of the paramyxovirus simian virus 5.

Adoptive transfer studies have shown that cytotoxic T lymphocytes (CTL) of high avidity, capable of recognizing low levels of peptide-MHC I molecules, are more efficient at reducing viral titers than are low-avidity CTL, thus establishing CTL avidity as a critical parameter for the ability of a CTL to clear virus in vivo. It has been well documented that CTL of high avidity are relatively CD8 independent, whereas low-avidity CTL require CD8 engagement in order to become activated. In this study we have analyzed the antiviral CTL response elicited following infection with the paramyxovirus simian virus 5 (SV5). We have identified the immunodominant and subdominant CTL responses and subsequently assessed the avidity of these responses by their CD8 dependence. This is the first study in which the relationship between immunodominance and CTL avidity has been investigated. The immunodominant response was directed against an epitope present in the viral M protein, and subdominant responses were directed against epitopes present in the P, F, and HN proteins. Similarly to other CTL responses we have analyzed, the immunodominant response and the subdominant F and HN responses were comprised of both high- and low-avidity CTL. However, the subdominant response directed against the epitope present in the P protein is novel, as it is exclusively high avidity. This high-avidity response is independent of both the route of infection and expression by recombinant SV5. A further understanding of the inherent properties of P that elicit only high-avidity CTL may allow for the design of more efficacious vaccine vectors that preferentially elicit high-avidity CTL in vivo.

Efficient generation of a reshaped human mAb specific for the alpha toxin of Clostridium perfringens.

We have used the technique of antibody reshaping to produce a humanized antibody specific for the alpha toxin of Clostridium perfringens. The starting antibody was from a mouse hybridoma from which variable (V) region nucleotide sequences were determined. The complementarity-determining regions (CDRs) from these V regions were then inserted into human heavy and light chain V region genes with human constant region gene fragments subsequently added. The insertion of CDRs alone into human frameworks did not produce a functional reshaped antibody and modifications to the V region framework were required. With minor framework modifications, the affinity of the original murine mAb was restored and even exceeded. Where affinity was increased, an altered binding profile to overlapping peptides was observed. Computer modelling of the reshaped heavy chain V regions suggested that amino acids adjacent to CDRs can either contribute to, or distort, CDR loop conformation and must be adjusted to achieve high binding affinity.