Gene recognition via spliced sequence alignment

Gene recognition is one of the most important problems in computational molecular biology. Previous attempts to solve this problem were based on statistics, and applications of combinatorial methods for gene recognition were almost unexplored. Recent advances in large-scale cDNA sequencing open a way toward a new approach to gene recognition that uses previously sequenced genes as a clue for recognition of newly sequenced genes. This paper describes a spliced alignment algorithm and software tool that explores all possible exon assemblies in polynomial time and finds the multiexon structure with the best fit to a related protein. Unlike other existing methods, the algorithm successfully recognizes genes even in the case of short exons or exons with unusual codon usage; we also report correct assemblies for genes with more than 10 exons. On a test sample of human genes with known mammalian relatives, the average correlation between the predicted and actual proteins was 99%. The algorithm correctly reconstructed 87% of genes and the rare discrepancies between the predicted and real exon-intron structures were caused either by short (less than 5 amino acids) initial/terminal exons or by alternative splicing. Moreover, the algorithm predicts human genes reasonably well when the homologous protein is nonvertebrate or even prokaryotic. The surprisingly good performance of the method was confirmed by extensive simulations: in particular, with target proteins at 160 accepted point mutations (PAM) (25% similarity), the correlation between the predicted and actual genes was still as high as 95%.     

CYP2D6 allelic frequencies in young-onset Parkinson's disease

Parkinson's disease (PD) is thought to develop as a result of interactions between genetic susceptibility factors and environmental exposures. One candidate gene is CYP2D6, which codes for the debrisoquine 4-hydroxylase cytochrome P450. Impairment of debrisoquine 4-hydroxylase activity has been associated with an increased risk of PD in patients with younger age at disease onset. Genotyping studies in patients with an older age at onset have reported modest increases in risk associated with the CYP2D6 B and A alleles; however, the risk for young-onset PD has not been adequately evaluated. We designed a case-control study to investigate the role of nonfunctional CYP2D6 allelic risk factors for young-onset PD in a sizable patient population and compared the distributions of CYP2D6 genotypes between young-onset ( < or = 51 years) PD patients (n = 108) and controls (n = 236). In contrast with the results from genotyping studies conducted among patients with an older age at onset, there were no significant differences in CYP2D6 allelic frequencies between young-onset PD cases and controls. The frequency of the B allele was slightly lower in the young-onset PD cases than in the controls (0.14 versus 0.20) (X2 = 2.66, p = 0.10). The presence of one or more B alleles was not associated with an increased risk of young-onset PD (odds ratio 0.58; 95% CI 0.33 to 1.00), nor was the presence of one or more nonfunctional alleles (i.e., A, B, D, and D2) (odds ratio 0.68; 95% CI 0.41 to 1.13). This study suggests that the young-onset PD population may differ from the older-onset population with respect to risk factors.     

Effects of hypothermia or anesthetics on hippocampal glutamate and glycine concentrations after repeated transient global cerebral ischemia

The reovirus group C temperature-sensitive mutant tsC447, whose defect maps to the S2 gene, which encodes the major core protein sigma 2, fails to assemble core particles at the nonpermissive temperature. To identify other proteins that may interact with sigma 2 during assembly, we generated and examined 10 independent revertants of the mutant. To determine which gene(s) carried a compensatory suppressor mutation(s), we generated intertypic reassortants between wild-type reovirus serotype 1 Lang and each revertant and determined the temperature sensitivities of the reassortants by efficiency-of-plating assays. Results of the efficiency-of-plating analyses indicated that reversion of the tsC447 defect was an intragenic process in all revertants. To identify the region(s) of sigma 2 that had reverted, we determined the nucleotide sequences of the S2 genes. In all revertant sequences examined, the G at nucleotide position 1166 in tsC447 had reverted to the A present in the wild-type sequence. This reversion leads to the restoration of a wild-type asparagine (in place of a mutant aspartic acid) at amino acid 383 in the sigma 2 sequence. These results collectively indicate that the functional lesion in tsC447 is Asp-383 and that this lesion cannot be corrected by alterations in other core proteins. These observations suggest that this region of sigma 2, which may be important in mediating assembly of the core particle, does not interact significantly with other reovirus proteins.     

Selective tumor kill of cerebral glioma by photodynamic therapy using a boronated porphyrin photosensitizer

The prognosis for patients with the high-grade cerebral glioma glioblastoma multiforme is poor. The median survival for primary tumors is < 12 months, with most recurring at the site of the original tumor, indicating that a more aggressive local therapy is required to eradicate the unresectable "nests" of tumor cells invading into adjacent brain. Two adjuvant therapies with the potential to destroy these cells are porphyrin-sensitized photodynamic therapy (PDT) and boron-sensitized boron neutron capture therapy (BNCT). The ability of a boronated porphyrin, 2,4-(alpha, beta-dihydroxyethyl) deuteroporphyrin IX tetrakiscarborane carboxylate ester (BOPP), to act as a photosensitizing agent was investigated in vitro with the C6 rat glioma cell line and in vivo with C6 cells grown as an intracerebral tumor after implantation into Wistar rats. These studies determined the doses of BOPP and light required to achieve maximal cell kill in vitro and selective tumor kill in vivo. The data show that BOPP is more dose effective in vivo by a factor of 10 than the current clinically used photosensitizer hematoporphyrin derivative and suggest that BOPP may have potential as a dual PDT/BNCT sensitizer.     

Policies, practices, and attitudes of North American medical journal editors

OBJECTIVE: To describe U.S. and Canadian medical journals, their editors, and policies that affect the dissemination of medical information. DESIGN: Mailed survey. PARTICIPANTS: Senior editors of all 269 leading medical journals published at least quarterly in the United States and Canada, of whom 221 (82%) responded. MAIN MEASURES: The questionnaire asked about characteristics of journal editors and their journals and about journals' policies toward peer review, conflicts of interest, prepublication discussions with the press, and pharmaceutical advertisements. RESULTS: The editors were overwhelmingly men (96%), middle-aged (mean age 61 years), and trained as physicians (82%). Although 98% claimed that their journals were "peer-reviewed," the editors differed in how they defined a "peer" and in the number of peers they deemed optimal for review. Sixty-three percent thought journals should check on reviewers' potential conflicts of interest, but only a minority supported masking authors' names and affiliations (46%), checking reviewers' financial conflicts of interest (40%), or revealing reviewers' names to authors (8%). The respondents advocated discussion of scientific findings with the press (84%), but only in accord with the Ingelfinger rule, i.e., after publication of the article (77%). Fifty-seven percent of the editors agreed that journals have a responsibility to ensure the truthfulness of pharmaceutical advertisements, and 40% favored subjecting advertisements to the same rigorous peer review as scientific articles. CONCLUSIONS: The responding editors were relatively homogeneous demographically and professionally, and they tended to support the editorial status quo. There was little sentiment in favor of tampering with the current peer-review system (however defined) or the Ingelfinger rule, but a surprisingly large percentage of the respondents favored more stringent review of drug advertisements.     

Market study: biomaterials supply for permanent medical implants

The withdrawal of DuPont as a supplier of key raw materials created a major dislocation in the medical device industry. We studied the present and future impact caused by the market removal of polyethylene terephthalate (PET) yarn ("Dacron"), polytetrafluorethylene (PTFE) fiber and resin ("Teflon"), and polyacetal resin ("Delrin"). Findings were: 1) Dollar values of the permanent medical implant markets for PET yarn, PTFE fiber and resin, and polyacetal resin are a minute fraction, of their values for their other commercial markets; 2) The implant market value is clearly not commensurate with the liability risk; and 3) The majority of these materials consumed by this market are used in the production of lifesaving, permanent medical implants [e.g., vital blood vessel replacements made from knitted polyester (PET)]. The remainder is used in life-enhancing, permanent implants [e.g., hernia patches made of polyester (PET) fabric].     

Novel interneuron having hybrid modulatory-central pattern generator properties in the feeding system of the snail, Lymnaea stagnalis

1. We used intracellular recording techniques to examine the role of a novel type of protraction phase interneuron, the lateral N1 (N1L) in the feeding system of the snail Lymnaea stagnalis. 2. The N1Ls are a bilaterally symmetrical pair of electrotonically coupled interneurons located in the buccal ganglia. Each N1L sends a single axon to the contralateral buccal ganglia. Their neurite processes are confined to the buccal neuropile. 3. In the isolated CNS, depolarization of an N1L is capable of driving a full (N1-->N2-->N3), fast (1 cycle every 5 s) fictive feeding rhythm. This was unlike the previously described N1 medial (N1M) central pattern generator (CPG) interneurons that were only capable of driving a slow, irregular rhythm. Attempts to control the frequency of the fictive feeding rhythm by injecting varying amounts of steady current into the N1Ls were unsuccessful. This contrasts with a modulatory neuron, the slow oscillator (SO), that has very similar firing patterns to the N1Ls, but where the frequency of the rhythm depends on the level of injected current. 4. The N1Ls' ability to drive a fictive feeding rhythm in the isolated preparation was due to their strong, monosynaptic excitatory chemical connection with the N1M CPG interneurons. Bursts of spikes in the N1Ls generated summating excitatory postsynaptic potentials (EPSPs) in the N1Ms to drive them to firing. The SO excited the N1M cells in a similar way, but the EPSPs are strongly facilitatory, unlike the N1L-->N1M connection. 5. Fast (1 cycle every 5 s) fictive feeding rhythms driven by the N1L occurred in the absence of spike activity in the SO modulatory neuron. In contrast, the N1L was usually active in SO-driven rhythms. 6. The ability of the SO to drive the N1L was due to strong electrotonic coupling, SO-->N1L. The weaker coupling in the opposite direction, N1L-->SO, did not allow the N1L to drive the SO. 7. Experiments on semintact lip-brain preparations allowed fictive feeding to be evoked by application of 0.1 M sucrose to the lips (mimicking the normal sensory input) rather than by injection of depolarizing current. Rhythmic bursting, characteristic of fictive feeding, began in both the SO and N1L at exactly the same time, indicating that these two cell types are activated in "parallel" to drive the feeding rhythm. 8. The N1L is also part of the CPG network. It Excited the N2s and inhibited the N3 phasic (N3p) and N3 tonic (N3t) CPG interneurons like the N1Ms.(ABSTRACT TRUNCATED AT 400 WORDS)     

Acute asthma: treatment and outcome of 2000 consecutive pediatric emergency room visits in Doha, Qatar

Caring for a "difficult patient" is a concern frequently communicated among nurses and reported in the clinical and research literature. A theoretical perspective explaining the phenomenon of difficult patients is proposed and is based on a reformulation of propositions from labeling theory and the concept of social deviance. Applications to nursing practice focus on patient characteristics judged as deviant by nurses, communication of the deviant label, and exclusionary and inclusionary reactions to perceived patient deviance.     

An investigation of semantic space in patients with schizophrenia

There has been increasing interest in the semantic cognitive system in schizophrenia. Recent findings suggest a possible breakdown of semantic information processing in this disorder. The current study attempts to further examine semantic organization in schizophrenia. Twenty-eight chronic, early-onset schizophrenic patients and 32 controls were matched for premorbid intelligence and compared in their ability to spontaneously cluster exemplars from a specific category during a fluency task. Using multidimensional scaling and clustering techniques, 11 exemplars occurring most frequently in both groups were chosen for examination of their relative "proximity" during word generation. Patients with schizophrenia showed a less stable two-dimensional organization of exemplars and were less likely to group exemplars into subordinate clusters than were normals. These results suggest that semantic networks are disorganized in these patients. These findings may have some implications for the debate over the origin of "thought disorder" in schizophrenia.     

Monokine products as predictors of AIDS dementia

OBJECTIVE: To determine whether or not soluble factors produced by peripheral blood mononuclear cells (PBMC) can predict AIDS dementia. DESIGN AND METHODS: PBMC were isolated from individuals with and without AIDS dementia complex (ADC) to determine if the levels of cytokines tumour necrosis factor (TNF)-alpha and interleukin (IL)-6, or the production of a neurotoxic substance, were significantly different. PBMC were studied after determining that the numbers of monocyte-derived macrophages isolated by adherence were highly variable from patients with ADC compared with individuals without ADC. We prospectively studied 16 AIDS dementia patients, 13 healthy HIV-seropositive individuals, and eight sero-negative controls. Supernatants from PBMC were assayed for TNF-alpha, IL-6 and alone for neurotoxicity on human neural cells in vitro. RESULTS: We observed a trend towards worse cognitive and motor performance in patients suffering from ADC but who had no opportunistic infections ('pure dementia'; n = 8). Levels of PBMC IL-6 were significantly higher in 'pure dementia' patients. There was a trend towards lower levels of PBMC TNF-alpha in the group of patients who had both dementia and opportunistic infections compared with "pure dementia' patients. Supernatant from PBMC of ADC patients was significantly more neurotoxic than that from healthy HIV-seropositive individuals. CONCLUSIONS: Macrophage isolation from PBMC of patients with ADC was altered. Soluble factors produced from PBMC were significantly more neurotoxic than soluble factors from PBMC of healthy HIV-seropositive individuals. PBMC production of TNF-alpha and IL-6 was not a significant predictor of ADC.