Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs

Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenotype. Structural variants (SVs), genomic alterations of 10 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to absence of clear reference genomes and presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing a single metagenome coassembly graph constructed from all samples in a series. The log fold change in graph coverage between subsequent samples is then calculated to call SVs that are thriving or declining throughout the series. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, which is particularly noticeable as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between subsequent time and temperature samples, suggesting host advantage. Our innovative approach leverages raw read patterns rather than references or MAGs to include all sequencing reads in analysis, and thus provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial genome dynamics.

Ti-15Mo Alloy Decreases the Stress Concentration in Mandibular Angle Fracture Internal Fixation Hardware

Objectives

Comparison of the mechanical stability of 2.0 plates made of commercially pure titanium (cpTi) and a titanium-molybdenum (Ti-15Mo) alloy and two methods of internal fixation employed mandibular angle fractures, using 3D finite element analysis.

Materials and Methods

Four groups were evaluated. For the cpTi: group Eng 1P, one 4-hole plate and 4 screws 6 mm long, in the tension zone of the mandible; group Eng 2P, two 4-hole plates, one in the tension zone of the mandible and the other in the compression zone, both were fixed with 8 screws 6 mm long. The same groups were created for the Ti-15Mo alloy. A 100 N compressive load was applied to the occlusal surface of the mandibular first molar on the plated side.

Results

When considering the von Mises equivalent stress (σ _vM) values for the comparison between both groups with one plate, a decrease of 10.5% in the plate and a decrease of 29.0% in the screws for the Ti-15Mo group was observed. Comparing the same groups with two plates, a decrease of 28.5% in the screws was shown for the Ti-15Mo alloy group. No significant differences were observed when considering maximum and minimum principal stresses (σ _max, σ _min), and maximum principal strain (ε _max) to the mandibular bone. The Ti-15Mo alloy plates substantially decreased the stress concentration in the screws for both internal fixation techniques and in the plate for the Ti-15Mo 1 plate group.

Conclusion

From a clinical standpoint, the use of Ti-Mo alloy with reduced stiffness will decrease the stress shielding between the hardware and bone, influencing the outcome of the treatment.

Soluble epoxide hydrolase inhibitor promotes immunomodulation to inhibit bone resorption

BACKGROUND AND OBJECTIVE

Soluble epoxide hydrolase (sEH) is an enzyme in the arachidonate cascade which converts epoxy fatty acids (EpFAs), such as epoxyeicosatrienoic acids (EETs) produced by cytochrome P450 enzymes, to dihydroxy-eicosatrienoic acids. In the last 20 years with the development of inhibitors to sEH it has been possible to increase the levels of EETs and other EpFAs in in vivo models. Recently, studies have shown that EETs play a key role in blocking inflammation in a bone resorption process, but the mechanism is not clear. In the current study we used the sEH inhibitor (1-trifluoromethoxyphenyl-3-(1-propionylpiperidin-4-yl) urea [TPPU]) to investigate the immunomodulatory effects in a mouse periodontitis model.

MATERIAL AND METHODS

Mice were infected on days 0, 2, and 4 with Aggregatibacter actinomycetemcomitans and divided into groups (n = 6) that were treated orally, daily for 15 days, with 1 mg/kg of TPPU. Then, the mice were killed and their jaws were analyzed for bone resorption using morphometry. Immunoinflammatory markers in the gingival tissue were analyzed by microarray PCR or western blotting.

RESULTS

Infected mice treated with TPPU showed lower bone resorption than infected mice without treatment. Interestingly, infected mice showed increased expression of sEH; however, mice treated with TPPU had a reduction in expression of sEH. Besides, several proinflammatory cytokines and molecular markers were downregulated in the gingival tissue in the group treated with 1 mg/kg of TPPU.

CONCLUSION

The sEH inhibitor, TPPU, showed immunomodulatory effects, decreasing bone resorption and inflammatory responses in a bone resorption mouse model.

Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement

Genome annotation is, nowadays, performed via automatic pipelines that cannot discriminate between right and wrong annotations. Given their importance in increasing the accuracy of the genome annotations of other organisms, it is critical that the annotations of model organisms reflect the current annotation gold standard. The genome of Bacillus subtilis strain 168 was sequenced twenty years ago. Using a combination of inductive, deductive and abductive reasoning, we present a unique, manually curated annotation, essentially based on experimental data. This reveals how this bacterium lives in a plant niche, while carrying a paleome operating system common to Firmicutes and Tenericutes. Dozens of new genomic objects and an extensive literature survey have been included for the sequence available at the INSDC (AccNum AL009126.3). We also propose an extension to Demerec's nomenclature rules that will help investigators connect to this type of curated annotation via the use of common gene names.

TLR9 activation is triggered by the excess of stimulatory versus inhibitory motifs present in Trypanosomatidae DNA

DNA sequences purified from distinct organisms, e.g. non vertebrate versus vertebrate ones, were shown to differ in their TLR9 signalling properties especially when either mouse bone marrow-derived- or human dendritic cells (DCs) are probed as target cells. Here we found that the DC-targeting immunostimulatory property of Leishmania major DNA is shared by other Trypanosomatidae DNA, suggesting that this is a general trait of these eukaryotic single-celled parasites. We first documented, in vitro, that the low level of immunostimulatory activity by vertebrate DNA is not due to its limited access to DCs' TLR9. In addition, vertebrate DNA inhibits the activation induced by the parasite DNA. This inhibition could result from the presence of competing elements for TLR9 activation and suggests that DNA from different species can be discriminated by mouse and human DCs. Second, using computational analysis of genomic DNA sequences, it was possible to detect the presence of over-represented inhibitory and under-represented stimulatory sequences in the vertebrate genomes, whereas L. major genome displays the opposite trend. Interestingly, this contrasting features between L. major and vertebrate genomes in the frequency of these motifs are shared by other Trypanosomatidae genomes (Trypanosoma cruzi, brucei and vivax). We also addressed the possibility that proteins expressed in DCs could interact with DNA and promote TLR9 activation. We found that TLR9 is specifically activated with L. major HMGB1-bound DNA and that HMGB1 preferentially binds to L. major compared to mouse DNA. Our results highlight that both DNA sequence and vertebrate DNA-binding proteins, such as the mouse HMGB1, allow the TLR9-signaling to be initiated and achieved by Trypanosomatidae DNA.

Influence of customized composite resin fibreglass posts on the mechanics of restored treated teeth

AIM

To evaluate the mechanical behaviour of the dentine/cement/post interface of a maxillary central incisor using the finite element method and to compare the stresses exerted using conventional or customized post cementation techniques.

METHODOLOGY

Four models of a maxillary central incisor were created using fibreglass posts cemented with several techniques: FGP1, a 1-mm-diameter conventionally cemented post; CFGP1, a 1-mm-diameter customized composite resin post; FGP2, a 2-mm-diameter conventionally cemented post; CFGP2, a 2-mm-diameter customized composite resin post. A distributed load of 1N was applied to the lingual aspect of the tooth at 45° to its long axis. Additionally, polymerization shrinkage of 1% was simulated for the resin cement. The surface of the periodontal ligament was fixed in the three axes (X =Y = Z = 0). The maximum principal stress (σ(max) ), minimum principal stress (σ(min)), equivalent von Mises stress (σ(vM) ) and shear stress (σ(shear)) were calculated for the dentine/cement/post interface using finite element software.

RESULTS

The peak of σ(max) for the cement layer occurred first in CFGP1 (1.77 MPa), followed by CFGP2 (0.99), FGP2 (0.44) and FGP1 (0.2). The shrinkage stress (σ(vM) ) of the cement layer occurred as follows: FGP1 (35 MPa), FGP2 (34), CFGP1 (30.7) and CFGP2 (30.1).

CONCLUSIONS

Under incisal loading, the cement layer of customized posts had higher stress concentrations. The conventional posts showed higher stress because of polymerization shrinkage.

Comparison of stress distribution between complete denture and implant-retained overdenture-2D FEA

The aim of this study was to compare the stress distribution induced by posterior functional loads on conventional complete dentures and implant-retained overdentures with different attachment systems using a two-dimentional Finite Element Analysis (FEA-2D). Three models representative of edentulous mandible were constructed on AutoCAD software; Group A (control), a model of edentulous mandible supporting a complete denture; Group B, a model of edentulous mandible supporting an overdenture over two splinted implants connected with the bar-clip system; Group C, a model of edentulous mandible supporting an overdenture over two unsplinted implants with the O-ring system. Evaluation was conducted on Ansys software, with a vertical force of 100 N applied on the mandibular left first molar. When the stress was evaluated in supporting tissues, groups B (51.0 MPa) and C (52.6 MPa) demonstrated higher stress values than group A (10.1 MPa). Within the limits of this study, it may be concluded that the use of an attachment system increased stress values; furthermore, the use of splinted implants associated with the bar-clip attachment system favoured a lower stress distribution over the supporting tissue than the unsplinted implants with an O-ring abutment to retain the mandibular overdenture.

Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction

We have reconstructed the gene content and order of the last common ancestor of the human pathogens Mycobacterium leprae and Mycobacterium tuberculosis. During the reductive evolution of M. leprae, 1537 of 2977 ancestral genes were lost, among which we found 177 previously unnoticed pseudogenes. We find evidence that a massive gene inactivation took place very recently in the M. leprae lineage, leading to the loss of hundreds of ancestral genes. A large proportion of their nucleotide content ( approximately 89%) still remains in the genome, which allowed us to characterize and date them. The age of the pseudogenes was computed using a new methodology based on the rates and patterns of substitution in the pseudogenes and functional orthologous genes of closely related genomes. The position of the genes that were lost in the ancestor's genome revealed that the process of function loss and degradation mainly took place through a gene-to-gene inactivation process, followed by the gradual loss of their DNA. This suggests a scenario of massive genome reduction through many nearly simultaneous pseudogenization events, leading to a highly specialized pathogen.

Longitudinal study of the influence of removable partial denture and chemical control on the levels of Streptococcus mutans in saliva

Some studies have evaluated the salivary levels of mutans streptococci (MS) in removable partial denture (RPD) users. Saliva samples (2.0 mL) were obtained from 31 patients in six periods: (T0): immediately before installation of RPD; (T8): 8 days after T0; (T48): 48 days after T0; (T92): 92 days after T0; (T140): 140 days after T0 and (T189): 189 days after T0. The samples were vortexed and serially diluted from 10(-1) to 10(-6) in 0.05 m phosphate buffer (pH 7.4). From each dilution, 0.025 mL was plated on Mitis Salivarius Bacitracin (MSB). The plates were incubated in 5% CO2 at 37 degrees C for 72 h. There was an increase (t-test, P < 0.05) in the number of MS between periods T0 and T48 (mean/s.d., CFU mL(-1) of saliva): T0: 2.26/4.43 x 10(6) and T48: 0.47/1.48 x 10(8). After this, intensive treatment with CHX was accomplished in 29 patients. Saliva samples were obtained after treatment in four periods: (T24 h): 24 h after T0; (T14): 14 days after T24 h; (T28): 28 days after T24 h, and (T63): 63 days after T24 h. The number of MS in saliva did not decrease (t-test, P > 0.05). A new CHX formulation was applied in 15 patients. Saliva samples were obtained in periods: (T0): before new CHX application; (T24 h): 24 h after T0 and (T82): 82 days after T0. The new CHX reduced MS levels in saliva: (mean/s.d., CFU mL(-1) of saliva): T0: 6.64/8.47 x 10(6) and T24 h: 3.2/4.27 x 10(5) (sign rank, P < 0.05). In conclusion, there was a significant increase in the number of MS in saliva after the installation of RPD. The intensive treatment with a properly formulated CHX was effective in the reduction of MS, between 24 h and 82 days after its application.

Ongoing evolution of strand composition in bacterial genomes

We tried to identify the substitutions involved in the establishment of replication strand bias, which has been recognized as an important evolutionary factor in the evolution of bacterial genomes. First, we analyzed the composition asymmetry of 28 complete bacterial genomes and used it to test the possibility that asymmetric deamination of cytosine might be at the origin of the bias. The model showed significant correlation to the data but left unexplained a significant portion of the variance and indicated a systematic underestimation of GC skews in comparison with TA skews. Second, we analyzed the substitutions acting on the genes from five fully sequenced Chlamydia genomes that had not suffered strand switch since speciation. This analysis showed that substitutions were not at equilibrium in Chlamydia trachomatis or in C. muridarum and that strand bias is still an on-going process in these genes. Third, we identified substitutions involved in the adaptation of genes that had switched strands after speciation. These genes adapted quickly to the skewed composition of the new strand, mostly due to C-->T, A-->G, and C-->G asymmetric substitutions. This observation was reinforced by the analysis of genes that switched strands after divergence between Bacillus subtilis and B. halodurans. Finally, we propose a more extended model based on the analysis of the substitution asymmetries of CHLAMYDIA: This model fits well with the data provided by bacterial genomes presenting strong strand bias.

Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis

Type II restriction modification systems (RMSs) have been regarded either as defense tools or as molecular parasites of bacteria. We extensively analyzed their evolutionary role from the study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of palindrome avoidance. This analysis reveals that palindrome avoidance is not universally spread among bacterial species and that it does not correlate with taxonomic proximity. Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome avoidance is intimately correlated with the infective behavior of the phage. We observe that the degree of palindrome and restriction site avoidance is significantly and consistently less important in phages than in their bacterial hosts. This result brings to the fore a larger selective load for palindrome and restriction site avoidance on the bacterial hosts than on their infecting phages. It is then consistent with a view where type II RMSs are considered as parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial third player in the host–parasite relationship between bacteria and phages.

Evolutionary role of restriction/modification systems as revealed by comparative genome analysis

Type II restriction modification systems (RMSs) have been regarded either as defense tools or as molecular parasites of bacteria. We extensively analyzed their evolutionary role from the study of their impact in the complete genomes of 26 bacteria and 35 phages in terms of palindrome avoidance. This analysis reveals that palindrome avoidance is not universally spread among bacterial species and that it does not correlate with taxonomic proximity. Palindrome avoidance is also not universal among bacteriophage, even when their hosts code for RMSs, and depends strongly on the genetic material of the phage. Interestingly, palindrome avoidance is intimately correlated with the infective behavior of the phage. We observe that the degree of palindrome and restriction site avoidance is significantly and consistently less important in phages than in their bacterial hosts. This result brings to the fore a larger selective load for palindrome and restriction site avoidance on the bacterial hosts than on their infecting phages. It is then consistent with a view where type II RMSs are considered as parasites possibly at the verge of mutualism. As a consequence, RMSs constitute a nontrivial third player in the host-parasite relationship between bacteria and phages.

The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis

Mycoplasma pulmonis is a wall-less eubacterium belonging to the Mollicutes (trivial name, mycoplasmas) and responsible for murine respiratory diseases. The genome of strain UAB CTIP is composed of a single circular 963 879 bp chromosome with a G + C content of 26.6 mol%, i.e. the lowest reported among bacteria, Ureaplasma urealyticum apart. This genome contains 782 putative coding sequences (CDSs) covering 91.4% of its length and a function could be assigned to 486 CDSs whilst 92 matched the gene sequences of hypothetical proteins, leaving 204 CDSs without significant database match. The genome contains a single set of rRNA genes and only 29 tRNAs genes. The replication origin oriC was localized by sequence analysis and by using the G + C skew method. Sequence polymorphisms within stretches of repeated nucleotides generate phase-variable protein antigens whilst a recombinase gene is likely to catalyse the site-specific DNA inversions in major M.pulmonis surface antigens. Furthermore, a hemolysin, secreted nucleases and a glyco-protease are predicted virulence factors. Surprisingly, several of the genes previously reported to be essential for a self-replicating minimal cell are missing in the M.pulmonis genome although this one is larger than the other mycoplasma genomes fully sequenced until now.

Effect of saccharin on antibacterial activity of chlorhexidine gel

Although chlorhexidine is the most effective agent against dental plaque it is extremely bitter. To prepare formulations, it is necessary to use flavoring and sweetening, which can inhibit the antibacterial effect of chlorhexidine. Saccharin has been considered a compatible substance to use in chlorhexidine rinse or gel preparations; however, the effect of a range of concentrations has not been studied. To evaluate the effect of different concentrations of saccharin on the antibacterial activity of chlorhexidine gel, hydroxy-ethyl-cellulose gels containing 1.0% chlorhexidine digluconate and 0.0 to 1.0% sodium saccharin were prepared. Activity against Streptococcus mutans was evaluated using the agar diffusion method and determination of MIC values. The inhibitory zones of growth were 7.83 +/- 0.54 mm when no saccharin was added to the chlorhexidine gel and 7.75 +/- 0.50, 7.63 +/- 0.48, 6.21 +/- 0.40, 4.13 +/- 0.38, when the concentrations of saccharin in the gels were 0.02, 0.10, 0.5, and 1.0%, respectively. The range of MIC values was 1-2 micrograms/ml, with saccharin concentrations of 0%, 0.02, and 0.1%. In contrast, the MIC values were 4-8 and 8-16 micrograms/ml with saccharin concentrations of 0.5% and 1.0%, respectively. The paired "t" test showed that 0.5 and 1.0% sodium saccharin inhibit the antibacterial activity of 1% digluconate chlorhexidine gel. These in vitro results suggest that saccharin may inhibit the efficacy of chlorhexidine against mutans streptococci, depending on the concentration.

Tracheostomy in children: there is a place for acceptable risk

BACKGROUND

Tracheostomy in children remains controversial regarding the risk of complications.

METHODS

Forty-six trauma patients (35 male and 11 female, mean age = 6.8 years) were admitted to the intensive care unit between 1987 and 1991 with severe head injury plus coma. Tracheostomy was performed with standard technique after 5.9 days (range, 2-12 days) of intubation.

RESULTS

There were no deaths from tracheostomy, but six deaths resulted from severe head injury. One child was discharged with tracheostomy. The 39 survivors remained with tracheostomy 16.14 days (range, 4-71 days) in the intensive care unit. After cannula removal, 31 remained asymptomatic; 8 had respiratory distress: 2 were normal, 5 had endoscopic treatment for subglottic granulomas/stenosis from intubation, and 1 had tracheomalacia from tracheostomy. In 1997, the 18 patients located for follow-up were asymptomatic. At endoscopy, 8 were normal, 9 had subglottal granulomas from intubation, and 1 had 20% tracheal stenosis from tracheostomy.

CONCLUSION

Most complications after tracheostomy result from intubation. Tracheostomy has an acceptable risk in children with severe head injury who need prolonged ventilatory support.

Sulphur islands in the Escherichia coli genome: markers of the cell's architecture?

Two highly contrasted images depict genomes: at first sight, genes appear to be distributed randomly along the chromosome. In contrast, their organisation into operons (or pathogenicity islands) suggests that, at least locally, related functions are in physical proximity. Analysis of the codon usage bias in orthologous genes in the genome of bacteria which diverged a long time ago suggested that some physical (architectural) selection pressure organised the distribution of genes along the chromosome. The metabolism of highly reactive species such as sulphur-containing molecules must be compartmentalised to escape the deleterious actions of diffusible reagents such as gases or radicals. We analysed the distribution of sulphur metabolism genes in the genome of Escherichia coli and found a number of them to be clustered into statistically significant islands. Another interesting feature of these genes is that the proteins they encode are significantly deprived of cysteine and methionine residues, as compared to the bulk proteins. We speculate that this clustering is associated to the organisation of sulphur metabolism proteins into islands where the sensitive sulphur-containing molecules are protected from reacting with elements in the environment such as dioxygen, nitric oxide or radicals.

Implication of gene distribution in the bacterial chromosome for the bacterial cell factory

As bacterial genome sequences accumulate, more and more pieces of data suggest that there is a significant correlation between the distribution of genes along the chromosome and the physical architecture of the cell, suggesting that the map of the cell is in the chromosome. Considering sequences and experimental data indicative of cell compartmentalisation, mRNA folding and turnover, as well as known structural features of protein and membrane complexes, we show that preliminary in silico analysis of whole genome sequences strongly substantiates this hypothesis. If there is a correlation between the genome sequence and the cell architecture, it must derive from some selection pressure in the organisms growing in the wild. As a consequence, the underlying constraints should be optimised in genetically modified organisms if one is to expect high product yields. Consequences in terms of gene expression for biotechnology are straightforward: knocking genes out and in genomes should not be randomly performed, but should follow the rules of chromosome organisation.

Functional and evolutionary roles of long repeats in prokaryotes

Most recently published complete bacterial genomes have revealed unexpectedly high numbers of long strict repeats. In this article we discuss the various functional and evolutionary roles of these repeats, focusing in particular on their role in terms of genome stability, gene transfer, and antigenic variation.

Codon usage and lateral gene transfer in Bacillus subtilis

Bacillus subtilis possesses three classes of genes, differing by their codon preference. One class corresponds to prophages or prophage-like elements, indicative of the existence of systematic lateral gene transfer in this organism. The nature of the selection pressure that operates on codon bias is beginning to be understood.

Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes

Prokaryotic genomes seem to be optimized toward compactness and have therefore been thought to lack long redundant DNA sequences. However, we identified a large number of long strict repeats in eight prokaryotic complete genomes and found that their density is negatively correlated with genome size. A detailed analysis of the long repeats present in the genome of Bacillus subtilis revealed a very strict constraint on the spatial distribution of repeats in this genome. We interpret this as the hallmark of selection processes leading to the addition of new genetic information. Such addition is independent of insertion sequences and relies on the nonspecific DNA uptake by the competent cell and its subsequent integration in the chromosome in a circular form through a Campbell-like mechanism. Similar patterns are found in other competent genomes of Gram-negative bacteria and Archaea, suggesting a similar evolutionary mechanism. The correlation of the spatial distribution of repeats and the absence of insertion sequences in a genome may indicate, in the framework of our model, that mechanisms aiming at their avoidance/elimination have been developed.

Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis

We analysed the Bacillus subtilis protein coding sequences termini, and compared it to other genomes. The analysis focused on signals, com-positional biases of nucleotides, oligonucleotides, codons and amino acids and mRNA secondary structure. AUG is the preferred start codon in all genomes, independent of their G+C content, and seems to induce less stable mRNA structures. However, it is not conserved between homologous genes neither is it preferred in highly expressed genes. In B.subtilis the ribosome binding site is very strong. We found that downstream boxes do not seem to exist either in Escherichia coli or in B.subtilis. UAA stop codon usage is correlated with the G+C content and is strongly selected in highly expressed genes. We found less stable mRNA structures at both termini, which we related to mRNA-ribosome and mRNA-release-factor interactions. This pattern seems to impose a peculiar A-rich nucleotide and codon usage bias in these regions. Finally the analysis of all proteins from B.subtilis revealed a similar amino acid bias near both termini of proteins consisting of over-representation of hydrophilic residues. This bias near the stop codon is partially release-factor specific.

Universal replication biases in bacteria

Analysis of 15 complete bacterial chromosomes revealed important biases in gene organization. Strong compositional asymmetries between the genes lying on the leading versus lagging strands were observed at the level of nucleotides, codons and, surprisingly, amino acids. For some species, the bias is so high that the sole knowledge of a protein sequence allows one to predict with almost no errors whether the gene is transcribed from one strand or the other. Furthermore, we show that these biases are not species specific but appear to be universal. These findings may have important consequences in our understanding of fundamental biological processes in bacteria, such as replication fidelity, codon usage in genes and even amino acid usage in proteins.

Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons

We present a general analysis of oligonucleotide usage in the complete genome of Bacillus subtilis . Several datasets were built in order to assign various biological contexts to the biased use of words and to reveal local asymmetries in word usage that may be coupled with replication, the control of gene expression and the restriction/modification system. This analysis was complemented by cross-comparisons with the complete genomes of Escherichia coli , Haemophilus influenzae and Methanococcus jannaschii . We have observed a large number of biased oligonucleotides for words of size up to 8, throughout the datasets and species, indicating that such long strict words play an important role as biological signals. We speculate that some of them are involved in interactions with DNA and/or RNA polymerases. An extensive analysis of palindrome abundances and distributions provides the surprising result that prophage-like elements embedded in the genome exhibit a smaller avoidance of restriction sites. This may reinforce a recently proposed hypothesis of a selfish gene phenomena in the transfer of restriction/modification systems in bacteria.

Comparison of 10 influenza A (H1N1 and H3N2) haemagglutinin sequences obtained directly from clinical specimens to those of MDCK cell- and egg-grown viruses

PCR was used to amplify and sequence the complete HA1 region of the haemagglutinin (HA)-encoding genes of 10 clinical isolates of influenza virus of the H1N1 or H3N2 subtypes. These sequences were compared to those obtained from viruses isolated from the same specimens after passage in eggs and MDCK cells. Amino acid substitutions in the egg-derived HA sequences were found in nine out of the 10 specimens analysed, whereas seven out of eight of the MDCK-derived HA sequences were identical to those in the corresponding original specimens. Changes in the H1 HA occurred at residues 77a, 196 (also found in the corresponding HA from the MDCK isolate), 225, 226 and 227; changes in the H3 HA occurred at residues 137, 156, 186, 248 and 276. In addition, we have shown that an amino acid change at residue 145 in the HA of the H3 subtype that was previously demonstrated to be egg-selected is now present in circulating strains.

Genetic and antigenic analyses of influenza A (H1N1) viruses, 1986-1991

Eighteen strains of human influenza A (H1N1) viruses isolated between August 1986 and January 1991 were analyzed in this study. Examination of the total viral genome of 12 strains by T1 mapping revealed that considerable genetic heterogeneity exists among these viruses. Partial sequencing of each of the non-HA RNA segments of 4 viruses having divergent T1 oligonucleotide maps indicated that only one was a reassortant virus that had genes from both the influenza A (H1N1) and (H3N2) subtypes. This reassortant obtained its PB2 gene from a virus of the H3N2 subtype and the other 7 RNA segments from an H1N1 parent. Sequencing studies of the HA1 domains of the hemagglutinin (HA) genes of these 18 strains revealed that although these viruses are antigenically similar to the reference strains A/Taiwan/1/86 and A/Singapore/6/86, 7 conserved amino acid substitutions that are shared by recently isolated H1N1 viruses have occurred in the main stream of evolution of the H1N1 subtype. Our data indicate that: (1) Genetic reassortment continues to contribute to genetic variability of H1N1 viruses. (2) Genetic variants of non-reassortant H1N1 viruses are co-circulating in the world. (3) The HA's of recent H1N1 viruses are related to those of the 1986 reference strains. (4) Although there has been little detectable antigenic variability, the HA genes of human epidemic influenza A (H1N1) viruses have continued to evolve at an evolutionary rate similar to that for the H1N1 and H3N2 viruses analyzed previously.

[Acute cardiorespiratory insufficiency due to electric injury: invasive hemodynamic study]

Case report on right branch block, acute pulmonary oedema and enteritis caused by electric shock in a boy. The invasive hemodynamic study showed primary pulmonary hypertension, cardiogenic shock, and acute respiratory failure. The outcome was good, with total and progressive recovery of all lesions. The literature review revealed the rarity of pulmonary oedema and enteritis after an electric shock. The invasive haemodynamic data suggest physiopathological explanations for findings in the case and indicate therapeutic measures for similar situations.

Laboratory characterization of a swine influenza virus isolated from a fatal case of human influenza

A swine influenza virus-like type A (H1N1) virus, designated A/Wisconsin/3523/88, was isolated in September 1988 from a Wisconsin woman who had died with primary viral pneumonia. Antigenic analyses with hemagglutinin-specific monoclonal antibodies and postinfection ferret serum indicated that the hemagglutinin of A/Wisconsin/3523/88 was antigenically closely related to viruses currently circulating in swine. Genetic analysis of the A/Wisconsin/3523/88 virus by RNA fingerprinting and partial RNA sequence analysis of seven of the eight segments indicated that the genome of the human isolate was similar to that of enzootic swine viruses. These laboratory data supported the epidemiologic findings that this human infection occurred by transmission of an enzootic swine influenza virus and that the virus showed no major genetic changes potentially related to increased pathogenesis.