Segmentation of yeast DNA using hidden Markov models

MOTIVATION

Compositionally homogeneous segments of genomic DNA often correspond to meaningful biological units. Simple sliding window analysis is usually insufficient for compositional segmentation of natural sequences. Hidden Markov models (HMM) with a small number of states are a natural language for description of compositional properties of chromosome-size DNA sequences.

RESULTS

The algorithms were applied to yeast Saccharomyces cerevisiae chromosomes (YC) I, III, IV, VI and IX. The optimal number of HMM states is found to be four. The optimal four-state HMMs for all chromosomes are very similar, as well as the reconstructed segmentations. In most cases the models with k + 1 states are obtained by 'splitting' one of the states in the model with k states, and the corresponding increase of the level of detail in segmentation. The high AT states usually correspond to intergenic regions. We also explore the model's likelihood landscape and analyze the dynamics of the optimization process, thus addressing the problem of reliability of the obtained optima and efficiency of the algorithms.

Frequent alternative splicing of human genes

Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes, yet the prevalence of alternative splicing has not been quantified. Here the spliced alignment algorithm was used to make a first inventory of exon-intron structures of known human genes using EST contigs from the TIGR Human Gene Index. The results on any one gene may be incomplete and will require verification, yet the overall trends are significant. Evidence of alternative splicing was shown in 35% of genes and the majority of splicing events occurred in 5' untranslated regions, suggesting wide occurrence of alternative regulation. Most of the alternative splices of coding regions generated additional protein domains rather than alternating domains.

Recognition of regulatory sites by genomic comparison

Availability of complete bacterial genomes opens the way to the comparative approach to the recognition of transcription regulatory sites. Assumption of regulon conservation in conjunction with profile analysis provides two lines of independent evidence making it possible to make highly specific predictions. Recently this approach was used to analyze several regulons in eubacteria and archaebacteria. The present review covers recent advances in the comparative analysis of transcriptional regulation in prokaryotes and phylogenetic fingerprinting techniques in eukaryotes, and describes the emerging patterns of the evolution of regulatory systems.

Statistical analysis of the exon-intron structure of higher and lower eukaryote genes

Statistics of the exon-intron structure and splicing sites of several diverse eukaryotes was studied. The yeast exon-intron structures have a number of unique features. A yeast gene usually have at most one intron. The branch site is strongly conserved, whereas the polypirimidine tract is short. Long yeast introns tend to have stronger acceptor sites. In other species the branch site is less conserved and often cannot be determined. In non-yeast samples there is an almost universal correlation between lengths of neighboring exons (all samples excluding protists) and correlation between lengths of neighboring introns (human, drosophila, protists). On the average first introns are longer, and anomalously long introns are usually first introns in a gene. There is a universal preference for exons and exon pairs with the (total) length divisible by 3. Introns positioned between codons are preferred, whereas those positioned between the first and second positions in codon are avoided. The choice of A or G at the third position of intron (the donor splice sites generally prefer purines at this position) is correlated with the overall GC-composition of the gene. In all samples dinucleotide AG is avoided in the region preceding the acceptor site.

Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes

Recognition of transcription regulation sites (operators) is a hard problem in computational molecular biology. In most cases, small sample size and low degree of sequence conservation preclude the construction of reliable recognition rules. We suggest an approach to this problem based on simultaneous analysis of several related genomes. It appears that as long as a gene coding for a transcription regulator is conserved in the compared bacterial genomes, the regulation of the respective group of genes (regulons) also tends to be maintained. Thus a gene can be confidently predicted to belong to a particular regulon in case not only itself, but also its orthologs in other genomes have candidate operators in the regulatory regions. This provides for a greater sensitivity of operator identification as even relatively weak signals are likely to be functionally relevant when conserved. We use this approach to analyze the purine (PurR), arginine (ArgR) and aromatic amino acid (TrpR and TyrR) regulons of Escherichia coli and Haemophilus influenzae. Candidate binding sites in regulatory regions of the respective H.influenzae genes are identified, a new family of purine transport proteins predicted to belong to the PurR regulon is described, and probable regulation of arginine transport by ArgR is demonstrated. Differences in the regulation of some orthologous genes in E.coli and H.influenzae, in particular the apparent lack of the autoregulation of the purine repressor gene in H.influenzae, are demonstrated.

ASDB: database of alternatively spliced genes

A database of alternatively spliced genes (ASDB) has been constructed based on (i) the results of the analysis of Swiss-Prot entries containing products of these genes and (ii) clustering procedure joining proteins that could arise by alternative splicing of the same gene. ASDB incorporates information about alternatively spliced genes, their products and expression patterns. It can be searched in order to find all products of alternative splicing produced in a particular tissue or a given organism, or all variants generated by a particular transcript. ASDB currently contains about 1700 protein sequences and can be accessed via the Internet at URL http://cbcg.nersc.gov/asdb

Performance-guarantee gene predictions via spliced alignment

An important and still unsolved problem in gene prediction is designing an algorithm that not only predicts genes but estimates the quality of individual predictions as well. Since experimental biologists are interested mainly in the reliability of individual predictions (rather than in the average reliability of an algorithm) we attempted to develop a gene recognition algorithm that guarantees a certain quality of predictions. We demonstrate here that the similarity level with a related protein is a reliable quality estimator for the spliced alignment approach to gene recognition. We also study the average performance of the spliced alignment algorithm for different targets on a complete set of human genomic sequences with known relatives and demonstrate that the average performance of the method remains high even for very distant targets. Using plant, fungal, and prokaryotic target proteins for recognition of human genes leads to accurate predictions with 95, 93, and 91% correlation coefficient, respectively. For target proteins with similarity score above 60%, not only the average correlation coefficient is very high (97% and up) but also the quality of individual predictions is guaranteed to be at least 82%. It indicates that for this level of similarity the worst case performance of the spliced alignment algorithm is better than the average case performance of many statistical gene recognition methods.

Algorithms and software for support of gene identification experiments

MOTIVATION

Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts.

RESULTS

The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.

Meningococcal cellulitis and sialadenitis

Neisseria meningitidis is a rare cause of cellulitis. No cases of meningococcal sialadenitis have previously been reported. We recently successfully treated a patient who had meningococcal cellulitis and sialadenitis. We review previously reported cases of cellulitis due to N meningitidis and speculate on the role of underlying disease in the pathogenesis of this infection.

Combinatorial approaches to gene recognition

Recognition of genes via exon assembly approaches leads naturally to the use of dynamic programming. We consider the general graph-theoretical formulation of the exon assembly problem and analyze in detail some specific variants: multicriterial optimization in the case of non-linear gene-scoring functions; context-dependent schemes for scoring exons and related procedures for exon filtering; and highly specific recognition of arbitrary gene segments, oligonucleotide probes and polymerase chain reaction (PCR) primers.

Encephalopathy due to capillary leak syndrome

Systemic capillary leak syndrome (SCLS) is characterized by intermittent attacks of leakage of intravascular fluids into the extravascular space. Hypovolemia, hemoconcentration, weakness, edema, and visceral congestion are resulting manifestations of SCLS. Most patients with SCLS have clear mentation during attacks, and encephalopathy is not a known manifestation of the syndrome. We report a patient with acute idiopathic capillary leak syndrome manifested in an acute encephalopathy. The possibility of SCLS should be considered in patients who have an encephalopathy and hemoconcentration.

Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes

Short palindromic sequences (4, 5 and 6 bp palindromes) are avoided at a statistically significant level in the genomes of several bacteria, including the completely sequenced Haemophilus influenzae and Synechocystis sp. genomes and in the complete genome of the archaeon Methanococcus jannaschii. In contrast, there is only moderate avoidance of palindromes in the small genome of the bacterium Mycoplasma genitalium and no detectable avoidance in the genomes of chloroplasts and mitochondria. The sites for type II restriction-modification enzymes detected in the given species tend to be among the most avoided palindromes in a particular genome, indicating a direct connection between the avoidance of short oligonucleotide words and restriction-modification systems with the respective specificity. Palindromes corresponding to sites for restriction enzymes from other species are also avoided, albeit less significantly, suggesting that in the course of evolution bacterial DNA has been exposed to a wide spectrum of restriction enzymes, probably as the result of lateral transfer mediated by mobile genetic elements, such as plasmids and prophages. Palindromic words appear to accumulate in DNA once it becomes isolated from restriction-modification systems, as demonstrated by the case of organellar genomes. By combining these observations with protein sequence analysis, we show that the most avoided 4-palindrome and the most avoided 6-palindrome in the archaeon M.jannaschii are likely to be recognition sites for two novel restriction-modification systems.

Fluconazole and amphotericin B for cryptococcal meningitis

OBJECTIVE

To describe a patient with cryptococcal meningitis treated with the combination of amphotericin B and fluconazole.

CASE SUMMARY

A 41-year-old woman with cryptococcal meningitis who was not infected with HIV was treated with a combination of amphotericin B and fluconazole because she did not respond to amphotericin B alone and could not tolerate amphotericin B with flucytosine. She improved clinically, but it is unclear whether the combination was beneficial.

DISCUSSION

Standard therapy for cryptococcal meningitis is amphotericin B with or without flucytosine. Fluconazole is an alternative therapy, but its efficacy has not been documented in the patient population not infected with HIV. Theoretically, the combination of amphotericin B and fluconazole is antagonistic, but in vitro and in vivo data suggest that antagonism may not occur. The combination of amphotericin B and fluconazole in cryptococcal meningitis has not been evaluated in clinical trials, and its use is not recommended.

CONCLUSIONS

A patient with cryptococcal meningitis was treated with the combination of amphotericin B and fluconazole because of a poor response to amphotericin B monotherapy and intolerance to flucytosine. It is unclear whether her clinical response was a result of the combination.

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%.

Peritonitis due to Penicillium sp in a patient receiving continuous ambulatory peritoneal dialysis

Infectious peritonitis is a common complication of continuous ambulatory peritoneal dialysis (CAPD). Only one case of CAPD-related peritonitis due to Penicillium sp has previously been reported. We present a second case in which fungal colonies were observed on the inner surface of the CAPD catheter. The infection was successfully treated with catheter removal and intravenous amphotericin B.

Recognition of genes in human DNA sequences

A new approach to computer-assisted gene recognition in higher eukaryote DNA is suggested. It allows one to use not only linear functions for scoring structures, but all functions satisfying natural monotonicity conditions. The algorithm constructs the set of structures guaranteed to contain an optimal structure for every function. So, it uncouples the time-consuming step of generation of this set from the fast step of structure scoring, thus making it simple to experiment with different functions. One particular scoring function, taking into account only codon usage and positional nucleotide frequencies of the splicing sites, has been implemented in the Genome Recognition and Exon Assembly Tool program, and has been tested on an independent sample of human genes, yielding 88% sensitivity and 79% specificity.

Streptococcal meningitis as a complication of diagnostic myelography: medicolegal aspects

Bacterial meningitis is a rare complication of myelography. Most reported cases of bacterial meningitis are caused by a wide variety of streptococcal species, but the source of these organisms is uncertain. We recently participated in the defense of two legal cases arising from this complication. We discuss the medicolegal aspects of streptococcal meningitis that is a complication of myelography.

Invasive staphylococcal infections complicating percutaneous transluminal coronary angioplasty: three cases and review

Infectious complications infrequently occur after percutaneous transluminal coronary angioplasty (PTCA) is performed. We recently treated three patients with invasive staphylococcal infections that developed after PTCA. Two patients had septic arthritis of the knee joint secondary to probable femoral endarteritis, and the third patient had an infected hematoma of the groin. Early reuse of the initial puncture site, prolonged retention of the femoral sheath, bleeding or hematoma at the femoral sheath insertion site and vascular complications such as pseudoaneurysm may predispose to infectious sequelae after PTCA. The clinician should be aware of these risks and the possibility that a patient may develop these potentially serious complications after PTCA.

In vitro killing of penicillin-susceptible, -intermediate, and -resistant strains of Streptococcus pneumoniae by cefotaxime, ceftriaxone, and ceftizoxime: a comparison of bactericidal and inhibitory activity with achievable CSF levels

This study assessed total microbial killing of 30 penicillin-susceptible, -intermediate, and -resistant strains of Streptococcus pneumoniae by cefotaxime, ceftriaxone, and ceftizoxime and compared these values with MICs for each strain against each agent as determined by three different methods/media. The results confirm the appropriateness of recent NCCLS recommendations for MIC interpretive criteria for third generation cephalosporins in which < or = 0.25 microgram/ml = susceptible and > or = 2.0 micrograms/ml = resistant when these agents are used to treat pneumococcal meningitis and data from total microbial killing studies suggests that most isolates with MICs of 0.5 and 1.0 mcg/ml would respond to high dose therapy with all three agents. The study also confirmed the recently described two- to four-fold decrease in activity of ceftizoxime against S. pneumoniae as compared with either cefotaxime or ceftriaxone; but noted that current NCCLS MIC interpretive criteria for the therapy of meningitis remain valid for all three agents. Finally, the study found that MICs determined by the E test or by microdilution broth methods using supplemented Todd Hewitt broth predict susceptibility as well as the NCCLS reference method. The actual selection among these agents for the therapy of pneumococcal meningitis should also consider other parameters including protein binding, age groups of clinical use, maximum potency against all clinically relevant pathogens, and cost.

Cefotaxime twice daily versus ceftriaxone once daily. A randomized controlled study in patients with serious infections

We randomized 365 patients with serious infections to treatment with either 2 g intravenously (IV) cefotaxime every 12 h or 2 g IV ceftriaxone once daily. Clinical response rates were similar in both treatment groups, with success defined as satisfactory or improved response in 107 of 124 (86.3%) evaluable patients in the cefotaxime group compared with 103 of 114 (90.4%) evaluable patients in the ceftriaxone group. Bacteriologic cure rates were also similar in the two groups (86.4%) in the cefotaxime group compared with 87.0% in the ceftriaxone group). There was no statistically significant difference in the incidence of drug-related adverse events in the two groups. These results indicate that 2 g cefotaxime twice daily is as effective, both clinically and bacteriologically, as 2 g ceftriaxone once daily in serious infections caused by susceptible pathogens.

Streptococcal meningitis complicating diagnostic myelography: three cases and review

Bacterial meningitis is a rare complication of myelography. Most reported cases are due to miscellaneous streptococci, but the source of these organisms is uncertain. The differential diagnosis of chemical meningitis caused by the contrast material vs. bacterial meningitis may be difficult. We recently treated three patients with streptococcal meningitis following myelography performed with the contrast medium iopamidol. We discuss the diagnostic and therapeutic approach to postmyelography meningitis.

Prediction of function in DNA sequence analysis

Recognition of function of newly sequenced DNA fragments is an important area of computational molecular biology. Here we present an extensive review of methods for prediction of functional sites, tRNA, and protein-coding genes and discuss possible further directions of research in this area.

Reconstruction of a string from substring precedence data

The problem of reconstructing of a symbol string given the data about precedence of fixed length substrings arises in the method of nucleic acid sequencing by nested strand hybridization. We reformulate the problem in the graph-theoretical terms, describe the structure of the set of solutions, and present polynomial time algorithms that check existence and uniqueness of a solution or finiteness of the solution set, and then construct the solutions.

Adenovirus parotitis in patients with AIDS

Adenoviruses are well documented as opportunistic pathogens in patients with immunocompromising conditions, including human immunodeficiency virus (HIV) infection. We recently diagnosed adenovirus infection of the parotid gland in two patients with AIDS. Viral cultures and electron microscopic examinations of parotid tissue were positive in both cases. Adenovirus infection should be considered in the differential diagnosis of parotid swelling in HIV-infected patients.

Bone marrow granulomas, fever, pancytopenia, and lupus-like syndrome due to tocainide

We describe the case of a patient in whom a syndrome of fever, pancytopenia, pleural effusion, hepatosplenomegaly, positive ANA antibodies, and bone marrow granulomas developed in association with tocainide therapy. Tocainide, a recognized, albeit rare, cause of fever, lupus-like syndrome, and cytopenias, should be added to the list of medications that can cause bone marrow granulomas.

Blastomycosis in immunocompromised patients

Among the endemic mycoses, blastomycosis has been least often associated with disorders of immune function, but the data presented herein suggest that blastomycosis may occur more commonly in immunocompromised patients than was previously recognized. We have observed a marked increased in the number of immunocompromised patients with blastomycosis over the last 15 years, increasing from about 3% of patients seen between 1956 and 1977 to almost 24% patients seen between 1978 and 1991. The disease appears to be much more aggressive in immunocompromised than in normal hosts. Almost 30% of the patients in our series died secondary to blastomycosis, with most deaths occurring within 5 weeks following the diagnosis. Furthermore, almost one third of those patients who died of other causes had evidence of persistent blastomycosis at death. Multiple organ and central nervous system involvement were relatively common in this series. For these reasons, early and aggressive therapy with amphotericin B is indicated for most immunocompromised patients with blastomycosis. Oral therapy with an azole compound should probably be reserved for patients who have responded to a primary course of amphotericin B but who require additional or long-term suppressive therapy. Until more data are available, the newer azoles should be used with caution as primary therapy in immunocompromised patients with blastomycosis, and considered only in patients with limited disease and a stable underlying condition. Caring for the immunocompromised patient poses many diagnostic and therapeutic challenges to the clinician, and among those patients who have been exposed to areas endemic for blastomycosis, B. dermatitidis must be regarded as a potentially important opportunistic pathogen.

A sequential study of intravenous and oral fleroxacin in the treatment of complicated urinary tract infection

This study enrolled patients with complicated urinary tract infections (UTIs) in a trial to determine the efficacy and safety of sequential therapy with intravenous fleroxacin (first 3 days) followed by oral fleroxacin, for a total course of 7-14 days, both administered at a dosage of 400 mg once a day. We enrolled 68 patients with complicated UTIs or acute pyelonephritis, 32 of whom were evaluable for bacteriologic and clinical efficacy. The pathogens isolated included Escherichia coli, 15; enterococci, 9; miscellaneous, 15. Intravenous fleroxacin was given for a mean of 3.2 days, followed by oral fleroxacin for a mean of 5.3 days. A total of 27 patients were clinically cured (84%), two improved, and three failed. A total of 26 patients were bacteriologically cured (81%), and six failed (19%). The bacteria that were not eradicated included enterococci, 4; Staphylococcus epidermidis, 1; and Pseudomonas species, 1. One enterococcal isolate became resistant to fleroxacin. Four patients were bacteremic (E. coli, 3; Proteus mirabilis, 1); the pathogen was eradicated in all cases. Two patients developed urinary enterococcal superinfections. A total of 12 patients experienced 16 adverse reactions remotely, possibly, or probably related to fleroxacin (insomnia, 3; dizziness, 2; miscellaneous, 11). One patient had a grand mal seizure after aspirating gastric contents; the seizure was thought to be only remotely related to the study drug. Fleroxacin was discontinued in two patients because of adverse effects (phlebitis at intravenous access site, 1; anxiety and insomnia, 1). Only minor and asymptomatic laboratory abnormalities were observed. All clinical and laboratory abnormalities resolved with discontinuation of the study drug. Fleroxacin is a safe and effective antibiotic for sequential intravenous and oral treatment of acute pyelonephritis and complicated UTIs. Enterococci may be problematic pathogens, as reported with other fluoroquinolones.

Statistical analysis and prediction of the exonic structure of human genes

Nonhomologous fully sequenced human protein-coding genes were studied. Three sets of exon-exon junctions were formed defined by the intron (shadow) position relative to the reading frame. For the analysis of intron shadow signals in exons, information content and discrimination energy approaches were used with the correction allowing one to ignore the influence of a protein-coding message. The corrected formulas allow one to define the consensuses for the three types of intron shadow signals as a AG/guwn, cAG/GUnn, and cAG/gunU, and provide better recognition than the original formulas. The analysis of the codon usage in the signal positions leads to the conclusion that the prevalence of some amino acids in corresponding protein sites is caused by the signal requirements and not vice versa. The distribution of potential intron shadow signals in exons contradicts the hypothesis of intron insertion into suitable preexisting sites. There exists a correlation between the intron types and/or the exon length modulo 3.

The rapid emergence of fluoroquinolone-methicillin-resistant Staphylococcus aureus infections in a community hospital. An in vitro look at alternative antimicrobial agents

The introduction of ciprofloxacin on an unrestricted basis into a 900-bed community hospital resulted in the emergence of high-level fluoroquinolone resistance among methicillin-resistant Staphylococcus aureus (MRSA) during the subsequent 18 months. Susceptibility testing revealed several old and new compounds to which all the S. aureus strains were susceptible. When an MRSA strain became resistant to ciprofloxacin it also exhibited high-level resistance to ofloxacin, fleroxacin, norfloxacin, and enoxacin. Two new experimental fluoroquinolones, WIN 57273 and CI-960, exhibited good activity against all test strains. Among the glycopeptide compounds, mupirocin and teicoplanin were approximately fourfold more active than vancomycin and ramoplanin. Rifampin and trimethoprim-sulfamethoxazole (TMP/SMZ) showed good activity against most strains as did imipenem. For clindamycin, gentamicin, and tetracycline susceptibilities exhibited a bimodal distribution with at least 10% of strains having resistant MIC values. Surprisingly, the addition of sulbactam potentiated the activity of ampicillin against the ciprofloxacin-resistant MRSA strains, however, sulbactam had little effect on cefoperazone activity against these same strains. Time-kill kinetic studies of selected antimicrobials against ciprofloxacin-resistant strains indicated good killing by vancomycin, ampicillin-sulbactam, and TMP/SMZ. Teicoplanin was less bactericidal than vancomycin while these same strains rapidly developed resistance to rifampin even at concentrations 8 x MIC. These data indicate certain alternative compounds within our study warrant further investigation, especially in vivo, against multiply-resistant staphylococci.

In vitro activity of various antimicrobial agents against Staphylococcus aureus isolates including fluoroquinolone- and oxacillin-resistant strains

To determine susceptibility to 31 old and new antimicrobials, 44 strains of Staphylococcus aureus, most resistant to oxacillin and ciprofloxacin and isolated in a community hospital, were tested in vitro. For the peptide/peptide-derivative compounds, with the exception of mersacidin, all strains were inhibited by less than or equal to 2 micrograms/ml. Minimum inhibitory concentration (MIC)90 values indicated mupirocin, teicoplanin, and MDL 62211 to be fourfold more active than vancomycin, ramoplanin, and decaplanin. For fluoroquinolones, ciprofloxacin-resistant S. aureus exhibited high-level cross-resistance to ofloxacin, norfloxacin, fleroxacin, enoxacin, and Ro 23-9424. WIN 57253, a new fluorinated naphthyridine, showed good activity against these strains. Among the beta-lactams, the penem-derivative compounds (imipenem, meropenem, FCE 22101, and HRE 664) had the greatest activity, although resistance to each compound was detected among oxacillin-resistant S. aureus. The presence of tazobactam reduced the piperacillin MIC90 fourfold. Oxacillin-susceptible strains were susceptible to cephalosporins/cephamycins, whereas most oxacillin-resistant strains exhibited resistance. This study has shown that certain old and new quinolones and peptide-derivative compounds have good in vitro activity against multiply resistant strains of S. aureus.

Nocardia otitidiscaviarum (caviae) infection in a heart transplant patient presented as having a thigh abscess (Madura thigh)

The first case of disseminated infection with Nocardia otitidiscaviarum in a heart transplant patient is reported. The clinical spectrum and treatment of infections with N. otitidiscaviarum is discussed, including our patient's apparent response to imipenem/cilastatin.

Subacute bacterial endocarditis secondary to Streptococcus pneumoniae

Pneumococcal endocarditis characteristically presents as an acute illness, often accompanied by purulent meningitis, rapid destruction of the heart valves, congestive heart failure, and high mortality. We describe two patients with subacute pneumococcal endocarditis without a known primary source of pneumococcal bacteremia, fever, meningitis, or congestive heart failure. Both patients were cured with medical therapy. Pneumococcal endocarditis can present as an indolent illness resembling viridans streptococcal endocarditis.

Extendable words in nucleotide sequences

Previous statistical analyses revealed several peculiarities of nucleotide sequences that preclude their description by existing models and thus allow one to distinguish DNA and RNA sequences from random A,T,G,C-texts. This is a consequence of the unusual distribution of certain words in nucleotide sequences: while the distribution of (most) words is consistent with Markov models of small orders, the distribution of certain words cannot be described by any previous model (anomalies in distribution of homonucleotide/homopurine/homopyrimidine runs, complementary and mirror palindromes, and non-stationary words). In this work we introduce a probabilistic approach that is partly motivated by analogy with linguistics. We also describe another important feature of DNA/RNA sequences: anomalies in distribution of words of poor nucleotide composition. We show that some classes of these words are the major obstacle for the simple Markov description of nucleotide sequences.

Spinal sepsis due to Streptococcus milleri: two cases and review

We have recently cared for two patients with spinal sepsis secondary to infection with Streptococcus milleri. One patient had a spinal epidural abscess and the other had meningitis as well as a spinal subdural empyema. A review of the English-language literature revealed only two previously reported cases of spinal epidural abscess due to S. milleri and no cases of spinal subdural empyema due to S. milleri. We report two cases of spinal sepsis due to S. milleri and discuss pertinent literature.

Computer prediction of the exon-intron structure of mammalian pre-mRNAs

A novel approach to the problem of prediction of protein-coding regions is suggested. This approach combines the site prediction methods to predict splicing sites and the global coding region prediction methods to choose the best variant of spliced mRNA. One of the advantages of the suggested algorithm is that the resulting mRNA or protein sequence may then be immediately analyzed further. The true mRNA either coincides with the predicted one or ranks high in the list of variants. In the latter situation the predicted mRNA usually differs from the true one in only one or two of several exons. The combined approach allows the use of a priori information (e.g. the putative protein length or the number of exons). It is possible to use additional parameters not considered here, such as the preferred lengths of exons and introns, and particularly the preferred position of introns in the reading frame and the preferred codon position of exon termini.

Fungal pseudomeningitis superimposed on Escherichia coli meningitis

Pseudomeningitis is the demonstration of microorganisms from the cerebrospinal fluid by stain or culture in a patient with symptoms suggesting meningitis. This is a report of fungal pseudomeningitis superimposed on a case of nosocomial Escherichia coli meningitis resulting from a neurosurgical procedure. Critical care personnel need to be aware of the possibility of pseudomeningitis with or without associated meningitis in the appropriate setting.